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Sample records for gemma functional subfamily

  1. CDD/SPARCLE: functional classification of proteins via subfamily domain architectures

    Science.gov (United States)

    Marchler-Bauer, Aron; Bo, Yu; Han, Lianyi; He, Jane; Lanczycki, Christopher J.; Lu, Shennan; Chitsaz, Farideh; Derbyshire, Myra K.; Geer, Renata C.; Gonzales, Noreen R.; Gwadz, Marc; Hurwitz, David I.; Lu, Fu; Marchler, Gabriele H.; Song, James S.; Thanki, Narmada; Wang, Zhouxi; Yamashita, Roxanne A.; Zhang, Dachuan; Zheng, Chanjuan; Geer, Lewis Y.; Bryant, Stephen H.

    2017-01-01

    NCBI's Conserved Domain Database (CDD) aims at annotating biomolecular sequences with the location of evolutionarily conserved protein domain footprints, and functional sites inferred from such footprints. An archive of pre-computed domain annotation is maintained for proteins tracked by NCBI's Entrez database, and live search services are offered as well. CDD curation staff supplements a comprehensive collection of protein domain and protein family models, which have been imported from external providers, with representations of selected domain families that are curated in-house and organized into hierarchical classifications of functionally distinct families and sub-families. CDD also supports comparative analyses of protein families via conserved domain architectures, and a recent curation effort focuses on providing functional characterizations of distinct subfamily architectures using SPARCLE: Subfamily Protein Architecture Labeling Engine. CDD can be accessed at https://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml. PMID:27899674

  2. Functional interactome of Aquaporin 1 sub-family reveals new physiological functions in Arabidopsis Thaliana

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    Mohamed Ragab Abdel Gawwad

    2013-09-01

    Full Text Available Aquaporins are channel proteins found in plasma membranes and intercellular membranes of different cellular compartments, facilitate the water flux, solutes and gases across the cellular plasma membranes. The present study highlights the sub-family plasma membrane intrinsic protein (PIP predicting the 3-D structure and analyzing the functional interactome of it homologs. PIP1 homologs integrate with many proteins with different plant physiological roles in Arabidopsis thaliana including; PIP1A and PIP1B: facilitate the transport of water, diffusion of amino acids and/or peptides from the vacuolar compartment to the cytoplasm, play a role in the control of cell turgor and cell expansion and involved in root water uptake respectively. In addition we found that PIP1B plays a defensive role against Pseudomonas syringae infection through the interaction with the plasma membrane Rps2 protein. Another substantial function of PIP1C via the interaction with PIP2E is the response to nematode infection. Generally, PIP1 sub-family interactome controlling many physiological processes in plant cell like; osmoregulation in plants under high osmotic stress such as under a high salt, response to nematode, facilitate the transport of water across cell membrane and regulation of floral initiation in Arabidopsis thaliana.

  3. The dual-function CD150 receptor subfamily: the viral attraction.

    Science.gov (United States)

    Sidorenko, Svetlana P; Clark, Edward A

    2003-01-01

    The CD150 subfamily within the CD2 family is a growing group of dual-function receptors that have within their cytoplasmic tails a characteristic signaling motif. The ITSM (immunoreceptor tyrosine-based switch motif) enables these receptors to bind to and be regulated by small SH2 domain adaptor proteins, including SH2D1A (SH2-containing adaptor protein SH2 domain protein 1A) and EAT-2 (EWS-activated transcript 2). A major signaling pathway through the prototypic receptor in this subfamily, CD150, leads to the activation of interferon-gamma, a key cytokine for viral immunity. As a result, many viruses have designed strategies to usurp or alter CD150 functions. Measles virus uses CD150 as a receptor and Molluscum contagiosum virus encodes proteins that are homologous to CD150. Thus, viruses use CD150 subfamily receptors to create a favorable environment to elude detection and destruction. Understanding the CD150 subfamily may lead to new strategies for vaccine development and antiviral therapies.

  4. Automated protein subfamily identification and classification.

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    Duncan P Brown

    2007-08-01

    Full Text Available Function prediction by homology is widely used to provide preliminary functional annotations for genes for which experimental evidence of function is unavailable or limited. This approach has been shown to be prone to systematic error, including percolation of annotation errors through sequence databases. Phylogenomic analysis avoids these errors in function prediction but has been difficult to automate for high-throughput application. To address this limitation, we present a computationally efficient pipeline for phylogenomic classification of proteins. This pipeline uses the SCI-PHY (Subfamily Classification in Phylogenomics algorithm for automatic subfamily identification, followed by subfamily hidden Markov model (HMM construction. A simple and computationally efficient scoring scheme using family and subfamily HMMs enables classification of novel sequences to protein families and subfamilies. Sequences representing entirely novel subfamilies are differentiated from those that can be classified to subfamilies in the input training set using logistic regression. Subfamily HMM parameters are estimated using an information-sharing protocol, enabling subfamilies containing even a single sequence to benefit from conservation patterns defining the family as a whole or in related subfamilies. SCI-PHY subfamilies correspond closely to functional subtypes defined by experts and to conserved clades found by phylogenetic analysis. Extensive comparisons of subfamily and family HMM performances show that subfamily HMMs dramatically improve the separation between homologous and non-homologous proteins in sequence database searches. Subfamily HMMs also provide extremely high specificity of classification and can be used to predict entirely novel subtypes. The SCI-PHY Web server at http://phylogenomics.berkeley.edu/SCI-PHY/ allows users to upload a multiple sequence alignment for subfamily identification and subfamily HMM construction. Biologists wishing to

  5. Structural and Functional Elucidation of Peptide Ts11 Shows Evidence of a Novel Subfamily of Scorpion Venom Toxins

    Science.gov (United States)

    Cremonez, Caroline M.; Maiti, Mohitosh; Peigneur, Steve; Cassoli, Juliana Silva; Dutra, Alexandre A. A.; Waelkens, Etienne; Lescrinier, Eveline; Herdewijn, Piet; de Lima, Maria Elena; Pimenta, Adriano M. C.; Arantes, Eliane C.; Tytgat, Jan

    2016-01-01

    To date, several families of peptide toxins specifically interacting with ion channels in scorpion venom have been described. One of these families comprise peptide toxins (called KTxs), known to modulate potassium channels. Thus far, 202 KTxs have been reported, belonging to several subfamilies of KTxs (called α, β, γ, κ, δ, and λ-KTxs). Here we report on a previously described orphan toxin from Tityus serrulatus venom, named Ts11. We carried out an in-depth structure-function analysis combining 3D structure elucidation of Ts11 and electrophysiological characterization of the toxin. The Ts11 structure is highlighted by an Inhibitor Cystine Knot (ICK) type scaffold, completely devoid of the classical secondary structure elements (α-helix and/or β-strand). This has, to the best of our knowledge, never been described before for scorpion toxins and therefore represents a novel, 6th type of structural fold for these scorpion peptides. On the basis of their preferred interaction with voltage-gated K channels, as compared to all the other targets tested, it can be postulated that Ts11 is the first member of a new subfamily, designated as ε-KTx. PMID:27706049

  6. Identification and Structure-Function Analysis of Subfamily Selective G Protein-Coupled Receptor Kinase Inhibitors

    Energy Technology Data Exchange (ETDEWEB)

    Homan, Kristoff T.; Larimore, Kelly M.; Elkins, Jonathan M.; Szklarz, Marta; Knapp, Stefan; Tesmer, John J.G. [Michigan; (Oxford)

    2015-02-13

    Selective inhibitors of individual subfamilies of G protein-coupled receptor kinases (GRKs) would serve as useful chemical probes as well as leads for therapeutic applications ranging from heart failure to Parkinson’s disease. To identify such inhibitors, differential scanning fluorimetry was used to screen a collection of known protein kinase inhibitors that could increase the melting points of the two most ubiquitously expressed GRKs: GRK2 and GRK5. Enzymatic assays on 14 of the most stabilizing hits revealed that three exhibit nanomolar potency of inhibition for individual GRKs, some of which exhibiting orders of magnitude selectivity. Most of the identified compounds can be clustered into two chemical classes: indazole/dihydropyrimidine-containing compounds that are selective for GRK2 and pyrrolopyrimidine-containing compounds that potently inhibit GRK1 and GRK5 but with more modest selectivity. The two most potent inhibitors representing each class, GSK180736A and GSK2163632A, were cocrystallized with GRK2 and GRK1, and their atomic structures were determined to 2.6 and 1.85 Å spacings, respectively. GSK180736A, developed as a Rho-associated, coiled-coil-containing protein kinase inhibitor, binds to GRK2 in a manner analogous to that of paroxetine, whereas GSK2163632A, developed as an insulin-like growth factor 1 receptor inhibitor, occupies a novel region of the GRK active site cleft that could likely be exploited to achieve more selectivity. However, neither compound inhibits GRKs more potently than their initial targets. This data provides the foundation for future efforts to rationally design even more potent and selective GRK inhibitors.

  7. Structural and Functional Analysis of a New Subfamily of Glycosyltransferases Required for Glycosylation of Serine-rich Streptococcal Adhesins

    Energy Technology Data Exchange (ETDEWEB)

    Zhu, Fan; Erlandsen, Heidi; Ding, Lei; Li, Jingzhi; Huang, Ying; Zhou, Meixian; Liang, Xiaobo; Ma, Jinbiao; Wu, Hui (UAB)

    2011-09-16

    Serine-rich repeat glycoproteins (SRRPs) are a growing family of bacterial adhesins found in many streptococci and staphylococci; they play important roles in bacterial biofilm formation and pathogenesis. Glycosylation of this family of adhesins is essential for their biogenesis. A glucosyltransferase (Gtf3) catalyzes the second step of glycosylation of a SRRP (Fap1) from an oral streptococcus, Streptococcus parasanguinis. Although Gtf3 homologs are highly conserved in SRRP-containing streptococci, they share minimal homology with functionally known glycosyltransferases. We report here the 2.3 {angstrom} crystal structure of Gtf3. The structural analysis indicates that Gtf3 forms a tetramer and shares significant structural homology with glycosyltransferases from GT4, GT5, and GT20 subfamilies. Combining crystal structural analysis with site-directed mutagenesis and in vitro glycosyltransferase assays, we identified residues that are required for UDP- or UDP-glucose binding and for oligomerization of Gtf3 and determined their contribution to the enzymatic activity of Gtf3. Further in vivo studies revealed that the critical amino acid residues identified by the structural analysis are crucial for Fap1 glycosylation in S. parasanguinis in vivo. Moreover, Gtf3 homologs from other streptococci were able to rescue the gtf3 knock-out mutant of S. parasanguinis in vivo and catalyze the sugar transfer to the modified SRRP substrate in vitro, demonstrating the importance and conservation of the Gtf3 homologs in glycosylation of SRRPs. As the Gtf3 homologs only exist in SRRP-containing streptococci, we conclude that the Gtf3 homologs represent a unique subfamily of glycosyltransferases.

  8. Modulating the function of ATP-binding cassette subfamily G member 2 (ABCG2) with inhibitor cabozantinib.

    Science.gov (United States)

    Zhang, Guan-Nan; Zhang, Yun-Kai; Wang, Yi-Jun; Barbuti, Anna Maria; Zhu, Xi-Jun; Yu, Xin-Yue; Wen, Ai-Wen; Wurpel, John N D; Chen, Zhe-Sheng

    2017-01-25

    Cabozantinib (XL184) is a small molecule tyrosine kinase receptor inhibitor, which targets c-Met and VEGFR2. Cabozantinib has been approved by the Food and Drug Administration to treat advanced medullary thyroid cancer and renal cell carcinoma. In the present study, we evaluated the ability of cabozantinib to modulate the function of the ATP-binding cassette subfamily G member 2 (ABCG2) by sensitizing cells that are resistant to ABCG2 substrate antineoplastic drugs. We used a drug-selected resistant cell line H460/MX20 and three ABCG2 stable transfected cell lines ABCG2-482-R2, ABCG2-482-G2, and ABCG2-482-T7, which overexpress ABCG2. Cabozantinib, at non-toxic concentrations (3 or 5μM), sensitized the ABCG2-overexpressing cells to mitoxantrone, SN-38, and topotecan. Our results indicate that cabozantinib reverses ABCG2-mediated multidrug resistance by antagonizing the drug efflux function of the ABCG2 transporter instead of downregulating its expression. The molecular docking analysis indicates that cabozantinib binds to the drug-binding site of the ABCG2 transporter. Overall, our findings demonstrate that cabozantinib inhibits the ABCG2 transporter function and consequently enhances the effect of the antineoplastic agents that are substrates of ABCG2. Cabozantinib may be a useful agent in anticancer treatment regimens for patients who are resistant to ABCG2 substrate drugs.

  9. The molecular evolution of the p120-catenin subfamily and its functional associations.

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    Robert H Carnahan

    Full Text Available BACKGROUND: p120-catenin (p120 is the prototypical member of a subclass of armadillo-related proteins that includes δ-catenin/NPRAP, ARVCF, p0071, and the more distantly related plakophilins 1-3. In vertebrates, p120 is essential in regulating surface expression and stability of all classical cadherins, and directly interacts with Kaiso, a BTB/ZF family transcription factor. METHODOLOGY/PRINCIPAL FINDINGS: To clarify functional relationships between these proteins and how they relate to the classical cadherins, we have examined the proteomes of 14 diverse vertebrate and metazoan species. The data reveal a single ancient δ-catenin-like p120 family member present in the earliest metazoans and conserved throughout metazoan evolution. This single p120 family protein is present in all protostomes, and in certain early-branching chordate lineages. Phylogenetic analyses suggest that gene duplication and functional diversification into "p120-like" and "δ-catenin-like" proteins occurred in the urochordate-vertebrate ancestor. Additional gene duplications during early vertebrate evolution gave rise to the seven vertebrate p120 family members. Kaiso family members (i.e., Kaiso, ZBTB38 and ZBTB4 are found only in vertebrates, their origin following that of the p120-like gene lineage and coinciding with the evolution of vertebrate-specific mechanisms of epigenetic gene regulation by CpG island methylation. CONCLUSIONS/SIGNIFICANCE: The p120 protein family evolved from a common δ-catenin-like ancestor present in all metazoans. Through several rounds of gene duplication and diversification, however, p120 evolved in vertebrates into an essential, ubiquitously expressed protein, whereas loss of the more selectively expressed δ-catenin, p0071 and ARVCF are tolerated in most species. Together with phylogenetic studies of the vertebrate cadherins, our data suggest that the p120-like and δ-catenin-like genes co-evolved separately with non-neural (E- and P

  10. The Hevea brasiliensis XIP aquaporin subfamily: genomic, structural and functional characterizations with relevance to intensive latex harvesting.

    Science.gov (United States)

    Lopez, David; Amira, Maroua Ben; Brown, Daniel; Muries, Beatriz; Brunel-Michac, Nicole; Bourgerie, Sylvain; Porcheron, Benoit; Lemoine, Remi; Chrestin, Hervé; Mollison, Ewan; Di Cola, Alessandra; Frigerio, Lorenzo; Julien, Jean-Louis; Gousset-Dupont, Aurélie; Fumanal, Boris; Label, Philippe; Pujade-Renaud, Valérie; Auguin, Daniel; Venisse, Jean-Stéphane

    2016-07-01

    X-Intrinsic Proteins (XIP) were recently identified in a narrow range of plants as a full clade within the aquaporins. These channels reportedly facilitate the transport of a wide range of hydrophobic solutes. The functional roles of XIP in planta remain poorly identified. In this study, we found three XIP genes (HbXIP1;1, HbXIP2;1 and HbXIP3;1) in the Hevea brasiliensis genome. Comprehensive bioinformatics, biochemical and structural analyses were used to acquire a better understanding of this AQP subfamily. Phylogenetic analysis revealed that HbXIPs clustered into two major groups, each distributed in a specific lineage of the order Malpighiales. Tissue-specific expression profiles showed that only HbXIP2;1 was expressed in all the vegetative tissues tested (leaves, stem, bark, xylem and latex), suggesting that HbXIP2;1 could take part in a wide range of cellular processes. This is particularly relevant to the rubber-producing laticiferous system, where this isoform was found to be up-regulated during tapping and ethylene treatments. Furthermore, the XIP transcriptional pattern is significantly correlated to latex production level. Structural comparison with SoPIP2;1 from Spinacia oleracea species provides new insights into the possible role of structural checkpoints by which HbXIP2;1 ensures glycerol transfer across the membrane. From these results, we discuss the physiological involvement of glycerol and HbXIP2;1 in water homeostasis and carbon stream of challenged laticifers. The characterization of HbXIP2;1 during rubber tree tapping lends new insights into molecular and physiological response processes of laticifer metabolism in the context of latex exploitation.

  11. New bounds on neutrino electric millicharge from GEMMA experiment on neutrino magnetic moment

    CERN Document Server

    Brudanin, Victor B; Starostin, Alexander S; Studenikin, Alexander I

    2014-01-01

    Using the new limit on the neutrino anomalous magnetic moment recently obtained by GEMMA experiment we get an order-of-magnitude estimation for possible new direct upper bound on the neutrino electric millicharge $\\mid q_{\

  12. Uncharacterized conserved motifs outside the HD-Zip domain in HD-Zip subfamily I transcription factors; a potential source of functional diversity

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    Cabello Julieta V

    2011-03-01

    role in their function, hence potentially constituting a major source of functional diversity among members of this subfamily.

  13. Characterization of the venom from the spider, Araneus gemma: search for a glutamate antagonist

    Energy Technology Data Exchange (ETDEWEB)

    Early, S.L.

    1985-01-01

    Venom from three spiders, Argiope aurantia, Neoscona arabesca, and Araneus gemma have been shown to inhibit the binding of L-(/sup 3/H)glutamate to both GBP and synaptic membranes. The venom from Araneus gemma was shown to be the most potent of the three venoms in inhibiting the binding of L-(/sup 3/H)glutamate to GBP. Therefore, Araneus gemma venom was selected for further characterization. Venom from Araneus gemma appeared to contain two factors which inhibit the binding of L-(/sup 3/H)glutamate to GBP and at least one factor that inhibits L-glutamate-stimulated /sup 35/SCN flux. Factor I is thought to be L-glutamic acid, based on: (1) its similar mobility to glutamic acid in thin-layer chromatography and amino acid analysis, (2) the presence of fingerprint molecular ion peaks for glutamate in the mass spectrum for the methanol:water (17:1) extract and for the fraction from the HPLC-purification of the crude venom, and (3) its L-glutamate-like interaction with the sodium-dependent uptake system. Factor II appears to be a polypeptide, possibly 21 amino acids in length, and does not appear to contain any free amino groups or tryptophan. While the venom does not appear to contain any indoleamines, three catecholamines (epinephrine, epinine, dopamine) and one catecholamine metabolite (DOPAC) were detected.

  14. Structural and functional analysis of a novel EstE5 belonging to the subfamily of hormone-sensitive lipase.

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    Nam, Ki Hyun; Kim, Min-Young; Kim, Soo-Jin; Priyadarshi, Amit; Lee, Won Ho; Hwang, Kwang Yeon

    2009-02-06

    Hormone-sensitive lipase (HSL) plays an important role in the regulation of rodent fat cell lipolysis. It is regarded as an adipose tissue-specific enzyme whose sole metabolic role is the catalysis of hormone-stimulated lipolysis in mammalian cells. In this report we describe the functional and structural analysis of an EstE5 protein from a soil metagenome library. Function analysis results indicated that EstE5 preferentially hydrolyzes short-chain ester compounds, and our kinetic studies revealed the optimal pH and temperature. Based on the structural analysis, we defined the active site and the binding pocket. Structurally, EstE5 belongs to the HSL family and these structural studies may have applications in the production of value-added products, including pharmaceuticals.

  15. The mammalian Rab family of small GTPases: definition of family and subfamily sequence motifs suggests a mechanism for functional specificity in the Ras superfamily.

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    Pereira-Leal, J B; Seabra, M C

    2000-08-25

    The Rab/Ypt/Sec4 family forms the largest branch of the Ras superfamily of GTPases, acting as essential regulators of vesicular transport pathways. We used the large amount of information in the databases to analyse the mammalian Rab family. We defined Rab-conserved sequences that we designate Rab family (RabF) motifs using the conserved PM and G motifs as "landmarks". The Rab-specific regions were used to identify new Rab proteins in the databases and suggest rules for nomenclature. Surprisingly, we find that RabF regions cluster in and around switch I and switch II regions, i.e. the regions that change conformation upon GDP or GTP binding. This finding suggests that specificity of Rab-effector interaction cannot be conferred solely through the switch regions as is usually inferred. Instead, we propose a model whereby an effector binds to RabF (switch) regions to discriminate between nucleotide-bound states and simultaneously to other regions that confer specificity to the interaction, possibly Rab subfamily (RabSF) specific regions that we also define here. We discuss structural and functional data that support this model and its general applicability to the Ras superfamily of proteins.

  16. Functional characterization of a first avian cytochrome P450 of the CYP2D subfamily (CYP2D49.

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    Hua Cai

    Full Text Available The CYP2D family members are instrumental in the metabolism of 20-25% of commonly prescribed drugs. Although many CYP2D isoforms have been well characterized in other animal models, research concerning the chicken CYP2Ds is limited. In this study, a cDNA encoding a novel CYP2D enzyme (CYP2D49 was cloned from the chicken liver for the first time. The CYP2D49 cDNA contained an open reading frame of 502 amino acids that shared 52%-57% identities with other CYP2Ds. The gene structure and neighboring genes of CYP2D49 are conserved and similar to those of human CYP2D6. Additionally, similar to human CYP2D6, CYP2D49 is un-inducible in the liver and expressed predominantly in the liver, kidney and small intestine, with detectable levels in several other tissues. Metabolic assays of the CYP2D49 protein heterologously expressed in E. coli and Hela cells indicated that CYP2D49 metabolized the human CYP2D6 substrate, bufuralol, but not debrisoquine. Moreover, quinidine, a potent inhibitor of human CYP2D6, only inhibited the bufuralol 1'-hydroxylation activity of CYP2D49 to a negligible degree. All these results indicated that CYP2D49 had functional characteristics similar to those of human CYP2D6 but measurably differed in the debrisoquine 4'-hydroxylation and quinidine inhibitory profile. Further structure-function investigations that employed site-directed mutagenesis and circular dichroism spectroscopy identified the importance of Val-126, Glu-222, Asp-306, Phe-486 and Phe-488 in keeping the enzymatic activity of CYP2D49 toward bufuralol as well as the importance of Asp-306, Phe-486 and Phe-488 in maintaining the conformation of CYP2D49 protein. The current study is only the first step in characterizing the metabolic mechanism of CYP2D49; further studies are still required.

  17. pkl1(+)and klp2(+): Two kinesins of the Kar3 subfamily in fission yeast perform different functions in both mitosis and meiosis.

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    Troxell, C L; Sweezy, M A; West, R R; Reed, K D; Carson, B D; Pidoux, A L; Cande, W Z; McIntosh, J R

    2001-11-01

    We have identified Klp2p, a new kinesin-like protein (KLP) of the KAR3 subfamily in fission yeast. The motor domain of this protein is 61% identical and 71% similar to Pkl1p, another fission yeast KAR3 protein, yet the two enzymes are different in behavior and function. Pkl1p is nuclear throughout the cell cycle, whereas Klp2p is cytoplasmic during interphase. During mitosis Klp2p enters the nucleus where it forms about six chromatin-associated dots. In metaphase-arrested cells these migrate back and forth across the nucleus. During early anaphase they segregate with the chromosomes into two sets of about three, fade, and are replaced by other dots that form on the spindle interzone. Neither klp2(+) nor pkl1(+) is essential, and the double deletion is also wild type for both vegetative and sexual reproduction. Each deletion rescues different alleles of cut7(ts), a KLP that contributes to spindle formation and elongation. When either or both deletions are combined with a dynein deletion, vegetative growth is normal, but sexual reproduction fails: klp2 Delta,dhc1-d1 in karyogamy, pkl1 Delta,dhc1-d1 in multiple phases of meiosis, and the triple deletion in both. Deletion of Klp2p elongates a metaphase-arrested spindle, but pkl1 Delta shortens it. The anaphase spindle of klp2 Delta becomes longer than the cell, leading it to curl around the cell's ends. Apparently, Klp2p promotes spindle disassembly and contributes to the behavior of mitotic chromosomes.

  18. Book review: Doing a Systematic Review: A Student's Guide, edited by Angela Boland, M. Gemma Cherry & Rumona Dickson

    NARCIS (Netherlands)

    S. Lecheler

    2014-01-01

    Writing a systematic review is one of the most challenging aspects of the academic process. With Doing a Systematic Review: A Student’s Guide, Angela Boland, M. Gemma Cherry and Rumona Dickson aim to offer a detailed and effective guide to writing a successful systematic review. This takes the book

  19. The structural biology of the FGF19 subfamily.

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    Beenken, Andrew; Mohammadi, Moosa

    2012-01-01

    The ability of the Fibroblast Growth Factor (FGF) 19 subfamily to signal in an endocrine fashion sets this subfamily apart from the remaining five FGF subfamilies known for their paracrine functions during embryonic development. Compared to the members of paracrine FGF subfamiles, the three members of the FGF19 subfamily, namely FGF19, FGF21 and FGF23, have poor affinity for heparan sulfate (HS) and therefore can diffuse freely in the HS-rich extracellular matrix to enter into the bloodstream. In further contrast to paracrine FGFs, FGF19 subfamily members have unusually poor affinity for their cognate FGF receptors (FGFRs) and therefore cannot bind and activate them in a solely HS-dependent fashion. As a result, the FGF19 subfamily requires α/βklotho coreceptor proteins in order to bind, dimerize and activate their cognate FGFRs. This klotho-dependency also determines the tissue specificity of endocrine FGFs. Recent structural and biochemical studies have begun to shed light onto the molecular basis for the klotho-dependent endocrine mode of action of the FGF19 subfamily. Crystal structures of FGF19 and FGF23 show that the topology of the HS binding site (HBS) of FGF19 subfamily members deviates drastically from the common topology adopted by the paracrine FGFs. The distinct topologies of the HBS of FGF19 and FGF23 prevent HS from direct hydrogen bonding with the backbone atoms of the HBS of these ligands and accordingly decrease the HS binding affinity of this subfamily. Recent biochemical data reveal that the ?klotho ectodomain binds avidly to the ectodomain of FGFR1c, the main cognate FGFR of FGF23, creating a de novo high affinity binding site for the C-terminal tail of FGF23. The isolated FGF23 C-terminus can be used to effectively inhibit the formation of the FGF23-FGFR1c-αklotho complex and alleviate hypophosphatemia in renal phosphate disorders due to elevated levels of FGF23.

  20. Novel biogenic aggregation of moss gemmae on a disappearing African glacier.

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    Jun Uetake

    Full Text Available Tropical regions are not well represented in glacier biology, yet many tropical glaciers are under threat of disappearance due to climate change. Here we report a novel biogenic aggregation at the terminus of a glacier in the Rwenzori Mountains, Uganda. The material was formed by uniseriate protonemal moss gemmae and protonema. Molecular analysis of five genetic markers determined the taxon as Ceratodon purpureus, a cosmopolitan species that is widespread in tropical to polar region. Given optimal growing temperatures of isolate is 20-30 °C, the cold glacier surface might seem unsuitable for this species. However, the cluster of protonema growth reached approximately 10 °C in daytime, suggesting that diurnal increase in temperature may contribute to the moss's ability to inhabit the glacier surface. The aggregation is also a habitat for microorganisms, and the disappearance of this glacier will lead to the loss of this unique ecosystem.

  1. GEMMA experiment: three years of the search for the neutrino magnetic moment

    CERN Document Server

    Beda, A G; Demidova, E V; Egorov, V G; Medvedev, D V; Shirchenko, M V; Starostin, A S; Vylov, Ts

    2009-01-01

    The result of the 3-year neutrino magnetic moment measurement at the Kalinin Nuclear Power Plant with the GEMMA spectrometer is presented. Antineutrino-electron scattering is investigated. A high-purity germanium detector of 1.5 kg placed at a distance of 13.9 m from the 3 GW(th) reactor core is used in the spectrometer. The antineutrino flux is 2.7E13 1/scm/s. The differential method is used to extract (nu-e) electromagnetic scattering events. The scattered electron spectra taken in 5184+6798 and 1853+1021 hours for the reactor ON and OFF periods are compared. The upper limit for the neutrino magnetic moment < 3.2E-11 Bohr magneton at 90% CL is derived from the data processing.

  2. The Results of Search for the Neutrino Magnetic Moment in GEMMA Experiment

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    A. G. Beda

    2012-01-01

    Full Text Available The result of the neutrino magnetic moment measurement at the Kalinin Nuclear Power Plant (KNPP with GEMMA spectrometer is presented. The antineutrino-electron scattering is investigated. A high-purity germanium detector with a mass of 1.5 kg placed at a distance of 13.9 m from the 3 GWth reactor core is exposed to the antineutrino flux of 2.7×1013 1/cm2/s. The recoil electron spectra taken in 18134 and 4487 hours for the reactor ON and OFF periods are compared. The upper limit for the neutrino magnetic moment μν<  2.9×10−11μB at 90% C.L. is derived from the data processing.

  3. Introducción del Operario Humano en el Ciclo de Automatización de Procesos Mediante la Guía GEMMA GEMMA Guide Approach for the Introduction of the Human Operator into the Automation Cycle

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    Pere Ponsa

    2007-01-01

    Full Text Available En este artículo, se presenta el estudio concreto de la intervención de operarios en sistemas automatizados a los que se ha aplicado la metodología llamada guía GEMMA (Estudio de Modos de Marchas y Paros. Siendo esta guía, una buena aproximación metodológica para resolver problemas complejos de automatización. Aunque su uso no es extenso, constituye una guía rigurosa que permite abordar la transición de los ejemplos académicos a las especificaciones industriales. La inclusión del operario humano, así como la comunicación con los dispositivos de automatización, necesita de guías metodológicas que puedan aunar la estructuración propuesta en la guía GEMMA con diversos conceptos extraídos de la ergonomía cognitiva y la interacción persona-ordenador. Se concluye que la guía GEMMA presenta una metodología integradora concebida para clarificar el rol del operario humano en el ciclo de automatización de sistemas complejos con aplicación en el control y supervisión de procesos industriales.The use of the design guide to start and stop modes, GEMMA guide, is known as a good approach to deal with the task of solving complex automation problems. Even not widely used, it constitutes a really good methodological approach that allows to smooth the transition from academical examples to industrial settings. The purpose of this paper is to show an additional advantage of the GEMMA guide that should motivate its use as well as introduce the consideration of the human operator as an integral part of the automation procedure. The inclusion of the human operator as well as his communication with the automation device needs some guidelines that can be drawn from joining the GEMMA structured approach with some concepts borrowed from cognitive ergonomic theory and human-computer interaction.

  4. Tetrahymena metallothioneins fall into two discrete subfamilies.

    Directory of Open Access Journals (Sweden)

    Silvia Díaz

    Full Text Available BACKGROUND: Metallothioneins are ubiquitous small, cysteine-rich, multifunctional proteins which can bind heavy metals. METHODOLOGY/PRINCIPAL FINDINGS: We report the results of phylogenetic and gene expression analyses that include two new Tetrahymena thermophila metallothionein genes (MTT3 and MTT5. Sequence alignments of all known Tetrahymena metallothioneins have allowed us to rationalize the structure of these proteins. We now formally subdivide the known metallothioneins from the ciliate genus Tetrahymena into two well defined subfamilies, 7a and 7b, based on phylogenetic analysis, on the pattern of clustering of Cys residues, and on the pattern of inducibility by the heavy metals Cd and Cu. Sequence alignment also reveals a remarkably regular, conserved and hierarchical modular structure of all five subfamily 7a MTs, which include MTT3 and MTT5. The former has three modules, while the latter has only two. Induction levels of the three T. thermophila genes were determined using quantitative real time RT-PCR. Various stressors (including heavy metals brought about dramatically different fold-inductions for each gene; MTT5 showed the highest fold-induction. Conserved DNA motifs with potential regulatory significance were identified, in an unbiased way, upstream of the start codons of subfamily 7a MTs. EST evidence for alternative splicing in the 3' UTR of the MTT5 mRNA with potential regulatory activity is reported. CONCLUSION/SIGNIFICANCE: The small number and remarkably regular structure of Tetrahymena MTs, coupled with the experimental tractability of this model organism for studies of in vivo function, make it an attractive system for the experimental dissection of the roles, structure/function relationships, regulation of gene expression, and adaptive evolution of these proteins, as well as for the development of biotechnological applications for the environmental monitoring of toxic substances.

  5. nES GEMMA Analysis of Lectins and Their Interactions with Glycoproteins - Separation, Detection, and Sampling of Noncovalent Biospecific Complexes

    Science.gov (United States)

    Engel, Nicole Y.; Weiss, Victor U.; Marchetti-Deschmann, Martina; Allmaier, Günter

    2017-01-01

    In order to better understand biological events, lectin-glycoprotein interactions are of interest. The possibility to gather more information than the mere positive or negative response for interactions brought mass spectrometry into the center of many research fields. The presented work shows the potential of a nano-electrospray gas-phase electrophoretic mobility molecular analyzer (nES GEMMA) to detect weak, noncovalent, biospecific interactions besides still unbound glycoproteins and unreacted lectins without prior liquid phase separation. First results for Sambucus nigra agglutinin, concanavalin A, and wheat germ agglutinin and their retained noncovalent interactions with glycoproteins in the gas phase are presented. Electrophoretic mobility diameters (EMDs) were obtained by nES GEMMA for all interaction partners correlating very well with molecular masses determined by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) of the individual molecules. Moreover, EMDs measured for the lectin-glycoprotein complexes were in good accordance with theoretically calculated mass values. Special focus was laid on complex formation for different lectin concentrations and binding specificities to evaluate the method with respect to results obtained in the liquid phase. The latter was addressed by capillary electrophoresis on-a-chip (CE-on-a-chip). Of exceptional interest was the fact that the formed complexes could be sampled according to their size onto nitrocellulose membranes after gas-phase separation. Subsequent immunological investigation further proved that the collected complex actually retained its native structure throughout nES GEMMA analysis and sampling.

  6. Subfamily logos: visualization of sequence deviations at alignment positions with high information content

    Directory of Open Access Journals (Sweden)

    Beitz Eric

    2006-06-01

    Full Text Available Abstract Background Recognition of relevant sequence deviations can be valuable for elucidating functional differences between protein subfamilies. Interesting residues at highly conserved positions can then be mutated and experimentally analyzed. However, identification of such sites is tedious because automated approaches are scarce. Results Subfamily logos visualize subfamily-specific sequence deviations. The display is similar to classical sequence logos but extends into the negative range. Positive, upright characters correspond to residues which are characteristic for the subfamily, negative, upside-down characters to residues typical for the remaining sequences. The symbol height is adjusted to the information content of the alignment position. Residues which are conserved throughout do not appear. Conclusion Subfamily logos provide an intuitive display of relevant sequence deviations. The method has proven to be valid using a set of 135 aligned aquaporin sequences in which established subfamily-specific positions were readily identified by the algorithm.

  7. Moving out: from sterol transport to drug resistance - the ABCG subfamily of efflux pumps.

    Science.gov (United States)

    Moitra, Karobi; Silverton, Latoya; Limpert, Katy; Im, Kate; Dean, Michael

    2011-01-01

    The ATP binding cassette (ABC) proteins are typically ATP-driven transmembrane pumps that have been evolutionarily conserved from bacteria to humans. In humans these transporters are subdivided into seven subfamilies, ranging from A to G. The ABCG subfamily of transporters is the primary focus of this review. This subfamily of proteins has been conserved throughout evolution and plays a central role in several cellular processes, such as sterol homeostasis and multidrug resistance. Functional polymorphisms/mutations in some of these G-subfamily transporters have clinical consequences in humans.

  8. Phylogenetic relationships and protein modelling revealed two distinct subfamilies of group II HKT genes between crop and model grasses.

    Science.gov (United States)

    Ariyarathna, H A Chandima K; Francki, Michael G

    2016-07-01

    Molecular evolution of large protein families in closely related species can provide useful insights on structural functional relationships. Phylogenetic analysis of the grass-specific group II HKT genes identified two distinct subfamilies, I and II. Subfamily II was represented in all species, whereas subfamily I was identified only in the small grain cereals and possibly originated from an ancestral gene duplication post divergence from the coarse grain cereal lineage. The core protein structures were highly analogous despite there being no more than 58% amino acid identity between members of the two subfamilies. Distinctly variable regions in known functional domains, however, indicated functional divergence of the two subfamilies. The subsets of codons residing external to known functional domains predicted signatures of positive Darwinian selection potentially identifying new domains of functional divergence and providing new insights on the structural function and relationships between protein members of the two subfamilies.

  9. Function of SSA subfamily of Hsp70 within and across species varies widely in complementing Saccharomyces cerevisiae cell growth and prion propagation.

    Directory of Open Access Journals (Sweden)

    Deepak Sharma

    Full Text Available BACKGROUND: The cytosol of most eukaryotic cells contains multiple highly conserved Hsp70 orthologs that differ mainly by their spatio-temporal expression patterns. Hsp70s play essential roles in protein folding, transport or degradation, and are major players of cellular quality control processes. However, while several reports suggest that specialized functions of Hsp70 orthologs were selected through evolution, few studies addressed systematically this issue. METHODOLOGY/PRINCIPAL FINDINGS: We compared the ability of Ssa1p-Ssa4p from Saccharomyces cerevisiae and Ssa5p-Ssa8p from the evolutionary distant yeast Yarrowia lipolytica to perform Hsp70-dependent tasks when expressed as the sole Hsp70 for S. cerevisiae in vivo. We show that Hsp70 isoforms (i supported yeast viability yet with markedly different growth rates, (ii influenced the propagation and stability of the [PSI(+] and [URE3] prions, but iii did not significantly affect the proteasomal degradation rate of CFTR. Additionally, we show that individual Hsp70 orthologs did not induce the formation of different prion strains, but rather influenced the aggregation properties of Sup35 in vivo. Finally, we show that [URE3] curing by the overexpression of Ydj1p is Hsp70-isoform dependent. CONCLUSION/SIGNIFICANCE: Despite very high homology and overlapping functions, the different Hsp70 orthologs have evolved to possess distinct activities that are required to cope with different types of substrates or stress situations. Yeast prions provide a very sensitive model to uncover this functional specialization and to explore the intricate network of chaperone/co-chaperone/substrates interactions.

  10. Extending the fossil record of Polytrichaceae: Early Cretaceous Meantoinea alophosioides gen. et sp. nov., permineralized gametophytes with gemma cups from Vancouver Island.

    Science.gov (United States)

    Bippus, Alexander C; Stockey, Ruth A; Rothwell, Gar W; Tomescu, Alexandru M F

    2017-04-01

    Diverse in modern ecosystems, mosses are dramatically underrepresented in the fossil record. Furthermore, most pre-Cenozoic mosses are known only from compression fossils, lacking detailed anatomical information. When preserved, anatomy vastly improves resolution in the systematic placement of fossils. Lower Cretaceous deposits at Apple Bay (Vancouver Island, British Columbia, Canada) contain a diverse anatomically preserved flora that includes numerous bryophytes, many of which have yet to be characterized. Among them is a polytrichaceous moss that is described here. Fossil moss gametophytes preserved in four carbonate concretions were studied in serial sections prepared using the cellulose acetate peel technique. We describe Meantoinea alophosioides gen. et sp. nov., a polytrichaceous moss with terminal gemma cups containing stalked, lenticular gemmae. Leaves with characteristic costal anatomy, differentiated into sheathing base and free lamina and bearing photosynthetic lamellae, along with a conducting strand in the stem, place Meantoinea in family Polytrichaceae. The bistratose leaf lamina with an adaxial layer of mamillose cells, short photosynthetic lamellae restricted to the costa, and presence of gemma cups indicate affinities with basal members of the Polytrichaceae, such as Lyellia, Bartramiopsis, and Alophosia. Meantoinea alophosioides enriches the documented moss diversity of an already-diverse Early Cretaceous plant fossil assemblage. This is the third moss described from the Apple Bay plant fossil assemblage and represents the first occurrence of gemma cups in a fossil moss. It is also the oldest unequivocal record of Polytrichaceae, providing a hard minimum age for the group of 136 million years. © 2017 Botanical Society of America.

  11. Pollen structure and function in caesalpinioid legumes.

    Science.gov (United States)

    Banks, Hannah; Rudall, Paula J

    2016-03-01

    A diverse range of pollen morphologies occurs within the large, paraphyletic legume subfamily Caesalpinioideae, especially among early-branching lineages. Previous studies have hypothesized an association between surface ornamentation and pollination syndrome or other aspects of pollen function such as desiccation tolerance and adaptations to accommodate volume changes. We reviewed caesalpinioid pollen morphology using light microscopy, scanning and transmission electron microscopy, in combination with a literature survey of pollination vectors. Pollen structural diversity is greatest in the early-branching tribes Cercideae and Detarieae, whereas Cassieae and Caesalpinieae are relatively low in pollen diversity. Functional structures to counter desiccation include opercula (lids) covering apertures and reduced aperture size. Structures preventing wall rupture during dehydration and rehydration include different forms of colpi (syncolpi, parasyncolpi, pseudocolpi), striate supratectal ornamentation, and columellate or granular wall structures that resist tensile or compressive forces respectively. Specialized aperture structures (Zwischenkörper) may be advantageous for efficient germination of the pollen tube. In Detarieae and Cercideae in particular, there is potential to utilize pollen characters to estimate pollination systems where these are unknown. Supratectal verrucae and gemmae have apparently evolved iteratively in Cercideae and Detarieae. At the species level, there is a potential correlation between striate/verrucate patterns and vertebrate pollination. © 2016 Botanical Society of America.

  12. Cytogenetics and genome evolution in the subfamily Triatominae (Hemiptera, Reduviidae).

    Science.gov (United States)

    Panzera, F; Pérez, R; Panzera, Y; Ferrandis, I; Ferreiro, M J; Calleros, L

    2010-01-01

    The subfamily Triatominae (Hemiptera, Reduviidae), vectors of Chagas disease, includes over 140 species. Karyotypic information is currently available for 80 of these species. This paper summarizes the chromosomal variability of the subfamily and how it may reveal aspects of genome evolution in this group. The Triatominae present a highly conserved chromosome number. All species, except 3, present 20 autosomes. The differences in chromosome number are mainly caused by variation in the number of sex chromosomes, due to the existence of 3 sex systems in males (XY, X(1)X(2)Y and X(1)X(2)X(3)Y). However, inter- and intraspecific differences in the position, quantity and meiotic behavior of constitutive heterochromatin, in the total genome size, and in the location of ribosomal 45S rRNA clusters, have revealed considerable cytogenetic variability within the subfamily. This cytogenetic diversity offers the opportunity to perform cytotaxonomic and phylogenetic studies, as well as structural, evolutionary, and functional analyses of the genome. The imminent availability of the complete genome of Rhodnius prolixus also opens new perspectives for understanding the evolution and genome expression of triatomines. The application of fluorescence in situ hybridization for the mapping of genes and sequences, as well as comparative analyses of genome homology by comparative genomic hybridization will be useful tools for understanding the genomic changes in relation to evolutionary processes such as speciation and adaptation to different environments.

  13. Combining gas-phase electrophoretic mobility molecular analysis (GEMMA), light scattering, field flow fractionation and cryo electron microscopy in a multidimensional approach to characterize liposomal carrier vesicles.

    Science.gov (United States)

    Urey, Carlos; Weiss, Victor U; Gondikas, Andreas; von der Kammer, Frank; Hofmann, Thilo; Marchetti-Deschmann, Martina; Allmaier, Günter; Marko-Varga, György; Andersson, Roland

    2016-11-20

    For drug delivery, characterization of liposomes regarding size, particle number concentrations, occurrence of low-sized liposome artefacts and drug encapsulation are of importance to understand their pharmacodynamic properties. In our study, we aimed to demonstrate the applicability of nano Electrospray Gas-Phase Electrophoretic Mobility Molecular Analyser (nES GEMMA) as a suitable technique for analyzing these parameters. We measured number-based particle concentrations, identified differences in size between nominally identical liposomal samples, and detected the presence of low-diameter material which yielded bimodal particle size distributions. Subsequently, we compared these findings to dynamic light scattering (DLS) data and results from light scattering experiments coupled to Asymmetric Flow-Field Flow Fractionation (AF4), the latter improving the detectability of smaller particles in polydisperse samples due to a size separation step prior detection. However, the bimodal size distribution could not be detected due to method inherent limitations. In contrast, cryo transmission electron microscopy corroborated nES GEMMA results. Hence, gas-phase electrophoresis proved to be a versatile tool for liposome characterization as it could analyze both vesicle size and size distribution. Finally, a correlation of nES GEMMA results with cell viability experiments was carried out to demonstrate the importance of liposome batch-to-batch control as low-sized sample components possibly impact cell viability. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

  14. The HRASLS (PLA/AT) subfamily of enzymes.

    Science.gov (United States)

    Mardian, Emily B; Bradley, Ryan M; Duncan, Robin E

    2015-10-26

    The H-RAS-like suppressor (HRASLS) subfamily consists of five enzymes (1-5) in humans and three (1, 3, and 5) in mice and rats that share sequence homology with lecithin:retinol acyltransferase (LRAT). All HRASLS family members possess in vitro phospholipid metabolizing abilities including phospholipase A1/2 (PLA1/2) activities and O-acyltransferase activities for the remodeling of glycerophospholipid acyl chains, as well as N-acyltransferase activities for the production of N-acylphosphatidylethanolamines. The in vivo biological activities of the HRASLS enzymes have not yet been fully investigated. Research to date indicates involvement of this subfamily in a wide array of biological processes and, as a consequence, these five enzymes have undergone extensive rediscovery and renaming within different fields of research. This review briefly describes the discovery of each of the HRASLS enzymes and their role in cancer, and discusses the biochemical function of each enzyme, as well as the biological role, if known. Gaps in current understanding are highlighted and suggestions for future research directions are discussed.

  15. The Ded1/DDX3 subfamily of DEAD-box RNA helicases.

    Science.gov (United States)

    Sharma, Deepak; Jankowsky, Eckhard

    2014-01-01

    In eukaryotic organisms, the orthologs of the DEAD-box RNA helicase Ded1p from yeast and DDX3 from human form a well-defined subfamily that is characterized by high sequence conservation in their helicase core and their N- and C- termini. Individual members of this Ded1/DDX3 subfamily perform multiple functions in RNA metabolism in both nucleus and cytoplasm. Ded1/DDX3 subfamily members have also been implicated in cellular signaling pathways and are targeted by diverse viruses. In this review, we discuss the considerable body of work on the biochemistry and biology of these proteins, including the recently discovered link of human DDX3 to tumorigenesis.

  16. Estimating diversence times among subfamilies in Nymphalidae

    Institute of Scientific and Technical Information of China (English)

    ZHANG Min; CAO TianWen; JIN Ke; REN ZhuMei; GUO YaPing; SHI Jing; ZHONG Yang; MA EnBo

    2008-01-01

    The mitochondrial cytochrome oxidase subunit I (COI) gene and the nuclear elongation factor 1α (EF-1α) gene were sequenced from 13 species of Nymphalidae. Phylogenetic trees of Nymphalidae, which is the largest family in butterflies, were constructed based on the sequences determined from 13 species sequenced in our laboratory and an additional 43 species obtained from GenBank using the maximum likelihood (ML) and Bayesian methods. Relative-rate tests between lineages in these phylogenetic trees were performed. On the basis of the results of the relative-rate tests and fossil information of Satyrinae, Nymphalinae and Biblidinae, the average divergence times among the subfamilies are estimated as 44.2-87.1 million years ago (Ma). These results will be helpful for better understanding of the origin and evolution of this family, as well as the divergence time of butterflies and other complex taxa.

  17. Actions and mode of actions of FGF19 subfamily members.

    Science.gov (United States)

    Fukumoto, Seiji

    2008-03-01

    Fibroblast growth factors (FGFs) are humoral factors with diverse biological functions. While most FGFs were shown to work as local factors regulating cell growth and differentiation, recent investigations indicated that FGF19 subfamily members, FGF15/19, FGF21 and FGF23 work as systemic factors. FGF15/19 produced by intestine inhibits bile acid synthesis and FGF21from liver is involved in carbohydrate and lipid metabolism. In addition, FGF23 was shown to be produced by bone and regulate phosphate and vitamin D metabolism. Furthermore, these FGFs require klotho or betaklotho for their actions in addition to canonical FGF receptors. It is possible that these FGFs together with their receptor systems might be targets for novel therapeutic measures in the future.

  18. Nano electrospray gas-phase electrophoretic mobility molecular analysis (nES GEMMA) of liposomes: applicability of the technique for nano vesicle batch control.

    Science.gov (United States)

    Weiss, Victor U; Urey, Carlos; Gondikas, Andreas; Golesne, Monika; Friedbacher, Gernot; von der Kammer, Frank; Hofmann, Thilo; Andersson, Roland; Marko-Varga, György; Marchetti-Deschmann, Martina; Allmaier, Günter

    2016-10-17

    Liposomes are biodegradable nanoparticle vesicles consisting of a lipid bilayer encapsulating an aqueous core. Entrapped cargo material is shielded from the extra-vesicular medium and sustained release of encapsulated material can be achieved. However, application of liposomes as nano-carriers demands their characterization concerning size and size distribution, particle-number concentration, occurrence of vesicle building blocks in solution and determination of the resulting vesicle encapsulation capacity. These questions can be targeted via gas-phase electrophoretic mobility molecular analysis (GEMMA) based on a nano electrospray (nES) charge-reduction source. This instrument separates single-charged nanoparticles in the gas-phase according to size in a high-laminar sheath-flow by means of an orthogonal, tunable electric field. nES GEMMA analysis enables to confirm liposome integrity after passage through the instrument (in combination with atomic force microscopy) as well as to exclude vesicle aggregation. Additionally, nanoparticle diameters at peak apexes and size distribution data are obtained. Differences of hydrodynamic and dry particle diameter values, as well as the effect of number- and mass-based concentration data analysis on obtained liposome diameters are shown. Furthermore, the repeatability of liposome preparation is studied, especially upon incorporation of PEGylated lipids in the bilayer. Finally, the instruments applicability to monitor mechanical stress applied to vesicles is demonstrated.

  19. Nano electrospray gas-phase electrophoretic mobility molecular analysis (nES GEMMA) of liposomes: applicability of the technique for nano vesicle batch control

    Science.gov (United States)

    Weiss, Victor U.; Urey, Carlos; Gondikas, Andreas; Golesne, Monika; Friedbacher, Gernot; von der Kammer, Frank; Hofmann, Thilo; Andersson, Roland; Marko-Varga, György; Marchetti-Deschmann, Martina

    2016-01-01

    Liposomes are biodegradable nanoparticle vesicles consisting of a lipid bilayer encapsulating an aqueous core. Entrapped cargo material is shielded from the extra-vesicular medium and sustained release of encapsulated material can be achieved. However, application of liposomes as nano-carriers demands their characterization concerning size and size distribution, particle-number concentration, occurrence of vesicle building blocks in solution and determination of the resulting vesicle encapsulation capacity. These questions can be targeted via gas-phase electrophoretic mobility molecular analysis (GEMMA) based on a nano electrospray (nES) charge-reduction source. This instrument separates single-charged nanoparticles in the gas-phase according to size in a high-laminar sheath-flow by means of an orthogonal, tunable electric field. nES GEMMA analysis enables to confirm liposome integrity after passage through the instrument (in combination with atomic force microscopy) as well as to exclude vesicle aggregation. Additionally, nanoparticle diameters at peak apexes and size distribution data are obtained. Differences of hydrodynamic and dry particle diameter values, as well as the effect of number- and mass-based concentration data analysis on obtained liposome diameters are shown. Furthermore, the repeatability of liposome preparation is studied, especially upon incorporation of PEGylated lipids in the bilayer. Finally, the instruments applicability to monitor mechanical stress applied to vesicles is demonstrated. PMID:27549027

  20. Evolution of substrate recognition sites (SRSs) in cytochromes P450 from Apiaceae exemplified by the CYP71AJ subfamily

    DEFF Research Database (Denmark)

    Dueholm, Bjørn; Krieger, Celia; Drew, Damian

    2015-01-01

    Background: Large proliferations of cytochrome P450 encoding genes resulting from gene duplications can be termed as 'blooms', providing genetic material for the genesis and evolution of biosynthetic pathways. Furanocoumarins are allelochemicals produced by many of the species in Apiaceaous plants...... belonging to the Apioideae subfamily of Apiaceae and have been described as being involved in the defence reaction against phytophageous insects. Results: A bloom in the cytochromes P450 CYP71AJ subfamily has been identified, showing at least 2 clades and 6 subclades within the CYP71AJ subfamily. Two...... of the subclades were functionally assigned to the biosynthesis of furanocoumarins. Six substrate recognition sites (SRS1-6) important for the enzymatic conversion were investigated in the described cytochromes P450 and display significant variability within the CYP71AJ subfamily. Homology models underline...

  1. Genesis of the vertebrate FoxP subfamily member genes occurred during two ancestral whole genome duplication events.

    Science.gov (United States)

    Song, Xiaowei; Tang, Yezhong; Wang, Yajun

    2016-08-22

    The vertebrate FoxP subfamily genes play important roles in the construction of essential functional modules involved in physiological and developmental processes. To explore the adaptive evolution of functional modules associated with the FoxP subfamily member genes, it is necessary to study the gene duplication process. We detected four member genes of the FoxP subfamily in sea lampreys (a representative species of jawless vertebrates) through genome screenings and phylogenetic analyses. Reliable paralogons (i.e. paralogous chromosome segments) have rarely been detected in scaffolds of FoxP subfamily member genes in sea lampreys due to the considerable existence of HTH_Tnp_Tc3_2 transposases. However, these transposases did not alter gene numbers of the FoxP subfamily in sea lampreys. The coincidence between the "1-4" gene duplication pattern of FoxP subfamily genes from invertebrates to vertebrates and two rounds of ancestral whole genome duplication (1R- and 2R-WGD) events reveal that the FoxP subfamily of vertebrates was quadruplicated in the 1R- and 2R-WGD events. Furthermore, we deduced that a synchronous gene duplication process occurred for the FoxP subfamily and for three linked gene families/subfamilies (i.e. MIT family, mGluR group III and PLXNA subfamily) in the 1R- and 2R-WGD events using phylogenetic analyses and mirror-dendrogram methods (i.e. algorithms to test protein-protein interactions). Specifically, the ancestor of FoxP1 and FoxP3 and the ancestor of FoxP2 and FoxP4 were generated in 1R-WGD event. In the subsequent 2R-WGD event, these two ancestral genes were changed into FoxP1, FoxP2, FoxP3 and FoxP4. The elucidation of these gene duplication processes shed light on the phylogenetic relationships between functional modules of the FoxP subfamily member genes.

  2. Nuclear/nucleolar GTPase 2 proteins as a subfamily of YlqF/YawG GTPases function in pre-60S ribosomal subunit maturation of mono- and dicotyledonous plants.

    Science.gov (United States)

    Im, Chak Han; Hwang, Sung Min; Son, Young Sim; Heo, Jae Bok; Bang, Woo Young; Suwastika, I Nengah; Shiina, Takashi; Bahk, Jeong Dong

    2011-03-11

    The YlqF/YawG families are important GTPases involved in ribosome biogenesis, cell proliferation, or cell growth, however, no plant homologs have yet to be characterized. Here we isolated rice (Oryza sativa) and Arabidopsis nuclear/nucleolar GTPase 2 (OsNug2 and AtNug2, respectively) that belong to the YawG subfamily and characterized them for pre-60S ribosomal subunit maturation. They showed typical intrinsic YlqF/YawG family GTPase activities in bacteria and yeasts with k(cat) values 0.12 ± 0.007 min(-1) (n = 6) and 0.087 ± 0.002 min(-1) (n = 4), respectively, and addition of 60S ribosomal subunits stimulated their activities in vitro. In addition, OsNug2 rescued the lethality of the yeast nug2 null mutant through recovery of 25S pre-rRNA processing. By yeast two-hybrid screening five clones, including a putative one of 60S ribosomal proteins, OsL10a, were isolated. Subcellular localization and pulldown assays resulted in that the N-terminal region of OsNug2 is sufficient for nucleolar/nuclear targeting and association with OsL10a. OsNug2 is physically associated with pre-60S ribosomal complexes highly enriched in the 25S, 5.8S, and 5S rRNA, and its interaction was stimulated by exogenous GTP. Furthermore, the AtNug2 knockdown mutant constructed by the RNAi method showed defective growth on the medium containing cycloheximide. Expression pattern analysis revealed that the distribution of AtNug2 mainly in the meristematic region underlies its potential role in active plant growth. Finally, it is concluded that Nug2/Nog2p GTPase from mono- and didicotyledonous plants is linked to the pre-60S ribosome complex and actively processed 27S into 25S during the ribosomal large subunit maturation process, i.e. prior to export to the cytoplasm.

  3. Evolution of substrate recognition sites (SRSs) in cytochromes P450 from Apiaceae exemplified by the CYP71AJ subfamily.

    Science.gov (United States)

    Dueholm, Bjørn; Krieger, Célia; Drew, Damian; Olry, Alexandre; Kamo, Tsunashi; Taboureau, Olivier; Weitzel, Corinna; Bourgaud, Frédéric; Hehn, Alain; Simonsen, Henrik Toft

    2015-06-26

    Large proliferations of cytochrome P450 encoding genes resulting from gene duplications can be termed as 'blooms', providing genetic material for the genesis and evolution of biosynthetic pathways. Furanocoumarins are allelochemicals produced by many of the species in Apiaceaous plants belonging to the Apioideae subfamily of Apiaceae and have been described as being involved in the defence reaction against phytophageous insects. A bloom in the cytochromes P450 CYP71AJ subfamily has been identified, showing at least 2 clades and 6 subclades within the CYP71AJ subfamily. Two of the subclades were functionally assigned to the biosynthesis of furanocoumarins. Six substrate recognition sites (SRS1-6) important for the enzymatic conversion were investigated in the described cytochromes P450 and display significant variability within the CYP71AJ subfamily. Homology models underline a significant modification of the accession to the iron atom, which might explain the difference of the substrate specificity between the cytochromes P450 restricted to furanocoumarins as substrates and the orphan CYP71AJ. Two subclades functionally assigned to the biosynthesis of furanocoumarins and four other subclades were identified and shown to be part of two distinct clades within the CYP71AJ subfamily. The subclades show significant variability within their substrate recognition sites between the clades, suggesting different biochemical functions and providing insights into the evolution of cytochrome P450 'blooms' in response to environmental pressures.

  4. Proteins with an alpha/beta hydrolase fold: Relationships between subfamilies in an ever-growing superfamily.

    Science.gov (United States)

    Lenfant, Nicolas; Hotelier, Thierry; Bourne, Yves; Marchot, Pascale; Chatonnet, Arnaud

    2013-03-25

    Alpha/beta hydrolases function as hydrolases, lyases, transferases, hormone precursors or transporters, chaperones or routers of other proteins. The amount of structural and functional available data related to this protein superfamily expands exponentially, as does the number of proteins classified as alpha/beta hydrolases despite poor sequence similarity and lack of experimental data. However the superfamily can be rationally divided according to sequence or structural homologies, leading to subfamilies of proteins with potentially similar functions. Since the discovery of proteins homologous to cholinesterases but devoid of enzymatic activity (e.g., the neuroligins), divergent functions have been ascribed to members of other subfamilies (e.g., lipases, dipeptidylaminopeptidase IV, etc.). To study the potentially moonlighting properties of alpha/beta hydrolases, the ESTHER database (for ESTerase and alpha/beta Hydrolase Enzymes and Relatives; http://bioweb.ensam.inra.fr/esther), which collects, organizes and disseminates structural and functional information related to alpha/beta hydrolases, has been updated with new tools and the web server interface has been upgraded. A new Overall Table along with a new Tree based on HMM models has been included to tentatively group subfamilies. These tools provide starting points for phylogenetic studies aimed at pinpointing the origin of duplications leading to paralogous genes (e.g., acetylcholinesterase versus butyrylcholinesterase, or neuroligin versus carboxylesterase). Another of our goals is to implement new tools to distinguish catalytically active enzymes from non-catalytic proteins in poorly studied or annotated subfamilies.

  5. Minimal subfamilies and the probabilistic interpretation for modulus on graphs

    CERN Document Server

    Albin, Nathan

    2016-01-01

    The notion of $p$-modulus of a family of objects on a graph is a measure of the richness of such families. We develop the notion of minimal subfamilies using the method of Lagrangian duality for $p$-modulus. We show that minimal subfamilies have at most $|E|$ elements and that these elements carry a weight related to their "importance" in relation to the corresponding $p$-modulus problem. When $p=2$, this measure of importance is in fact a probability measure and modulus can be thought as trying to minimize the expected overlap in the family.

  6. Gene Structures, Classification, and Expression Models of the DREB Transcription Factor Subfamily in Populus trichocarpa

    Directory of Open Access Journals (Sweden)

    Yunlin Chen

    2013-01-01

    Full Text Available We identified 75 dehydration-responsive element-binding (DREB protein genes in Populus trichocarpa. We analyzed gene structures, phylogenies, domain duplications, genome localizations, and expression profiles. The phylogenic construction suggests that the PtrDREB gene subfamily can be classified broadly into six subtypes (DREB A-1 to A-6 in Populus. The chromosomal localizations of the PtrDREB genes indicated 18 segmental duplication events involving 36 genes and six redundant PtrDREB genes were involved in tandem duplication events. There were fewer introns in the PtrDREB subfamily. The motif composition of PtrDREB was highly conserved in the same subtype. We investigated expression profiles of this gene subfamily from different tissues and/or developmental stages. Sixteen genes present in the digital expression analysis had high levels of transcript accumulation. The microarray results suggest that 18 genes were upregulated. We further examined the stress responsiveness of 15 genes by qRT-PCR. A digital northern analysis showed that the PtrDREB17, 18, and 32 genes were highly induced in leaves under cold stress, and the same expression trends were shown by qRT-PCR. Taken together, these observations may lay the foundation for future functional analyses to unravel the biological roles of Populus’ DREB genes.

  7. Organization and evolution of two SIDER retroposon subfamilies and their impact on the Leishmania genome

    Directory of Open Access Journals (Sweden)

    Bringaud Frédéric

    2009-05-01

    Full Text Available Abstract Background We have recently identified two large families of extinct transposable elements termed Short Interspersed DEgenerated Retroposons (SIDERs in the parasitic protozoan Leishmania major. The characterization of SIDER elements was limited to the SIDER2 subfamily, although members of both subfamilies have been shown to play a role in the regulation of gene expression at the post-transcriptional level. Apparent functional domestication of SIDERs prompted further investigation of their characterization, dissemination and evolution throughout the Leishmania genus, with particular attention to the disregarded SIDER1 subfamily. Results Using optimized statistical profiles of both SIDER1 and SIDER2 subgroups, we report the first automated and highly sensitive annotation of SIDERs in the genomes of L. infantum, L. braziliensis and L. major. SIDER annotations were combined to in-silico mRNA extremity predictions to generate a detailed distribution map of the repeat family, hence uncovering an enrichment of antisense-oriented SIDER repeats between the polyadenylation and trans-splicing sites of intergenic regions, in contrast to the exclusive sense orientation of SIDER elements within 3'UTRs. Our data indicate that SIDER elements are quite uniformly dispersed throughout all three genomes and that their distribution is generally syntenic. However, only 47.4% of orthologous genes harbor a SIDER element in all three species. There is evidence for species-specific enrichment of SIDERs and for their preferential association, especially for SIDER2s, with different metabolic functions. Investigation of the sequence attributes and evolutionary relationship of SIDERs to other trypanosomatid retroposons reveals that SIDER1 is a truncated version of extinct autonomous ingi-like retroposons (DIREs, which were functional in the ancestral Leishmania genome. Conclusion A detailed characterization of the sequence traits for both SIDER subfamilies unveils

  8. Relevance of the NR4A sub-family of nuclear orphan receptors in trophoblastic BeWo cell differentiation.

    Science.gov (United States)

    Malhotra, Sudha Saryu; Gupta, Satish Kumar

    2017-01-01

    Nur-77, a member of the NR4A sub-family of nuclear orphan receptors, is downregulated in the placentae of pre-eclamptic women. Here, we investigate the relevance of Nor-1, Nurr-1 and Nur-77 in trophoblastic cell differentiation. Their transcript levels were found to be significantly upregulated in BeWo cells treated with forskolin. The maximum increase was observed after 2 h, with a second peak in the expression levels after 48 h. The expression of NR4A sub-family members was also found to be upregulated in BeWo cells after treatment with hCG and GnRH. A similar significant increase was observed at the respective protein levels after 2 and 48 h of treatment with forskolin, hCG or GnRH. Silencing Nor-1, Nurr-1 or Nur-77 individually did not show any effect on forskolin-, hCG- and/or GnRH-mediated BeWo cell fusion and/or hCG secretion. After silencing any one member of the NR4A sub-family, an increase in the transcript levels of the other sub-family members was observed, indicating a compensatory effect due to their functional redundancy. Simultaneously silencing all three NR4A sub-family members significantly downregulated forskolin- and hCG-mediated BeWo cell fusion and/or hCG secretion. However, a considerable amount of cell death occurred after forskolin or hCG treatment as compared to the control siRNA-transfected cells. These results suggest that the NR4A sub-family of nuclear orphan receptors has a role in trophoblastic cell differentiation.

  9. Vaillantellinae, A New Subfamily Of Cobitidae (Pisces, Cypriniformes)

    NARCIS (Netherlands)

    Nalbant, T.T.; Banarescu, P.M.

    1977-01-01

    INTRODUCTION It is generally accepted that the Eurasian freshwater fish family Cobitidae includes three main divisions, usually considered as subfamilies: Cobitinae, Botiinae and Noemacheilinae (Berg, 1940; Ramaswami, 1953; Nalbant, 1963). The two first named, in which the lateral ethmoids are movab

  10. First molecular phylogeny of the subfamily Polycerinae (Mollusca, Nudibranchia, Polyceridae)

    Science.gov (United States)

    Palomar, Gemma; Pola, Marta; Garcia-Vazquez, Eva

    2014-03-01

    The subfamily Polycerinae includes four genera with around 46 species described to date. This subfamily is characterized by a limaciform body, which may have simple tentacular processes on the margin of the oral veil. Phylogenetic relationships between the genera of the subfamily Polycerinae (Polyceridae) have not yet been studied, and therefore, the only available information is based on morphological descriptions. The present study reports the first phylogenetic analysis of Polycerinae based on the mitochondrial genes cytochrome oxidase subunit I and the large ribosomal subunit (16S rRNA) using maximum likelihood and Bayesian methods. Our results showed that Polycerinae is monophyletic, but the relationships within the subfamily as well as within Polycera remain unresolved. A key finding of this study is that there are clearly two sympatric species of Polycera present in South Africa: Polycera capensis Quoy and Gaimard, 1824 also found in Australia and an undescribed Polycera sp. On the other hand, the studied specimens of the genus Gymnodoris were clustered within Polycerinae, reopening the problem of the systematic position of this genus. Additional genes and species of Polycerinae and Gymnodoris would provide more information and probably fully resolve this situation.

  11. Identification and Characterization of the Populus AREB/ABF Subfamily

    Institute of Scientific and Technical Information of China (English)

    Lexiang Ji; Jia Wang; Meixia Ye; Ying Li; Bin Guo; Zhong Chen; Hao Li; Xinmin An

    2013-01-01

    Abscisic acid (ABA) is a major plant hormone that plays an important role in responses to abiotic stresses.The ABA-responsive element binding proteinlABRE-binding factor (AREB/ABF) gene subfamily contains crucial transcription factors in the ABA-mediated signaling pathway.In this study,a total of 14 putative AREB/ABF members were identified in the Populus trichocarpa Torr.& Gray.genome using five AREB/ABF amino acid sequences from Arabidopsis thaliana L.as probes.The 14 putative Populus subfamily members showed high protein similarities,especially in the basic leucine zipper (bZlP) domain region.A neighbor-joining analysis combined with gene structure data revealed homology among the 14 genes.The expression patterns of the Populus AREB/ABF subfamily suggested that the most abundant transcripts of 11 genes occurred in leaf tissues,while two genes were most transcribed in root tissues.Significantly,eight Populus AREB/ABF gene members were upregulated after treatment with 100 μM exogenous ABA,while the other six members were downregulated.We identified the expression profiles of the subfamily members in Populus tissues and elucidated different response patterns of Populus AREB/ABF members to ABA stress.This study provided insight into the roles of Populus AREB/ABF homologues in plant response to abiotic stresses.

  12. Prevalent Exon-Intron Structural Changes in the APETALA1/FRUITFULL, SEPALLATA, AGAMOUS-LIKE6, and FLOWERING LOCUS C MADS-Box Gene Subfamilies Provide New Insights into Their Evolution.

    Science.gov (United States)

    Yu, Xianxian; Duan, Xiaoshan; Zhang, Rui; Fu, Xuehao; Ye, Lingling; Kong, Hongzhi; Xu, Guixia; Shan, Hongyan

    2016-01-01

    AP1/FUL, SEP, AGL6, and FLC subfamily genes play important roles in flower development. The phylogenetic relationships among them, however, have been controversial, which impedes our understanding of the origin and functional divergence of these genes. One possible reason for the controversy may be the problems caused by changes in the exon-intron structure of genes, which, according to recent studies, may generate non-homologous sites and hamper the homology-based sequence alignment. In this study, we first performed exon-by-exon alignments of these and three outgroup subfamilies (SOC1, AG, and STK). Phylogenetic trees reconstructed based on these matrices show improved resolution and better congruence with species phylogeny. In the context of these phylogenies, we traced evolutionary changes of exon-intron structures in each subfamily. We found that structural changes have occurred frequently following gene duplication and speciation events. Notably, exons 7 and 8 (if present) suffered more structural changes than others. With the knowledge of exon-intron structural changes, we generated more reasonable alignments containing all the focal subfamilies. The resulting trees showed that the SEP subfamily is sister to the monophyletic group formed by AP1/FUL and FLC subfamily genes and that the AGL6 subfamily forms a sister group to the three abovementioned subfamilies. Based on this topology, we inferred the evolutionary history of exon-intron structural changes among different subfamilies. Particularly, we found that the eighth exon originated before the divergence of AP1/FUL, FLC, SEP, and AGL6 subfamilies and degenerated in the ancestral FLC-like gene. These results provide new insights into the origin and evolution of the AP1/FUL, FLC, SEP, and AGL6 subfamilies.

  13. Autoinhibitory Interdomain Interactions and Subfamily-specific Extensions Redefine the Catalytic Core of the Human DEAD-box Protein DDX3.

    Science.gov (United States)

    Floor, Stephen N; Condon, Kendall J; Sharma, Deepak; Jankowsky, Eckhard; Doudna, Jennifer A

    2016-01-29

    DEAD-box proteins utilize ATP to bind and remodel RNA and RNA-protein complexes. All DEAD-box proteins share a conserved core that consists of two RecA-like domains. The core is flanked by subfamily-specific extensions of idiosyncratic function. The Ded1/DDX3 subfamily of DEAD-box proteins is of particular interest as members function during protein translation, are essential for viability, and are frequently altered in human malignancies. Here, we define the function of the subfamily-specific extensions of the human DEAD-box protein DDX3. We describe the crystal structure of the subfamily-specific core of wild-type DDX3 at 2.2 Å resolution, alone and in the presence of AMP or nonhydrolyzable ATP. These structures illustrate a unique interdomain interaction between the two ATPase domains in which the C-terminal domain clashes with the RNA-binding surface. Destabilizing this interaction accelerates RNA duplex unwinding, suggesting that it is present in solution and inhibitory for catalysis. We use this core fragment of DDX3 to test the function of two recurrent medulloblastoma variants of DDX3 and find that both inactivate the protein in vitro and in vivo. Taken together, these results redefine the structural and functional core of the DDX3 subfamily of DEAD-box proteins.

  14. Nuclear phylogenomics of the palm subfamily Arecoideae (Arecaceae).

    Science.gov (United States)

    Comer, Jason R; Zomlefer, Wendy B; Barrett, Craig F; Stevenson, Dennis Wm; Heyduk, Karolina; Leebens-Mack, James H

    2016-04-01

    Palms (Arecaceae) include economically important species such as coconut, date palm, and oil palm. Resolution of the palm phylogeny has been problematic due to rapid diversification and slow rates of molecular evolution. The focus of this study is on relationships of the 14 tribes of subfamily Arecoideae and their inferred ancestral areas. A targeted sequencing approach was used to generate a data set of 168 single/low copy nuclear genes for 34 species representing the Arecoideae tribes and the other palm subfamilies. Species trees from the concatenated and coalescent based analyses recovered largely congruent topologies. Three major tribal clades were recovered: the POS clade (Podococceae, Oranieae, Sclerospermeae), the RRC clade (Roystoneeae, Reinhardtieae, Cocoseae), and the core arecoid clade (Areceae, Euterpeae, Geonomateae, Leopoldinieae, Manicarieae, Pelagodoxeae). Leopoldinieae was sister to the rest of the core arecoids (Geonomateae, Manicarieae+Pelagodoxeae, and Areceae+Euterpeae). The nuclear phylogeny supported a North American origin for subfamily Arecoideae, with most tribal progenitors diversifying within the Americas. The POS clade may have dispersed from the Americas into Africa, with tribe Oranieae subsequently spreading into the Indo-Pacific. Two independent dispersals into the Indo-Pacific were inferred for two tribes within the core arecoids (tribes Areceae and Pelagodoxeae).

  15. The Subfamily-Specific Interaction between Kv2.1 and Kv6.4 Subunits Is Determined by Interactions between the N- and C-termini

    OpenAIRE

    Elke Bocksteins; Evy Mayeur; Abbi Van Tilborg; Glenn Regnier; Jean-Pierre Timmermans; Snyders, Dirk J

    2014-01-01

    The "silent" voltage-gated potassium (KvS) channel subunit Kv6.4 does not form electrically functional homotetramers at the plasma membrane but assembles with Kv2.1 subunits, generating functional Kv2.1/Kv6.4 heterotetramers. The N-terminal T1 domain determines the subfamily-specific assembly of Kv1-4 subunits by preventing interactions between subunits that belong to different subfamilies. For Kv6.4, yeast-two-hybrid experiments showed an interaction of the Kv6.4 N-terminus with the Kv2.1 N-...

  16. A genomic view of the NOD-like receptor family in teleost fish: Identification of a novel NLR subfamily in zebrafish

    Science.gov (United States)

    Laing, K.J.; Purcell, M.K.; Winton, J.R.; Hansen, J.D.

    2008-01-01

    Background. A large multigene family of NOD-like receptor (NLR) molecules have been described in mammals and implicated in immunity and apoptosis. Little information, however, exists concerning this gene family in non-mammalian taxa. This current study, therefore, provides an in-depth investigation of this gene family in lower vertebrates including extensive phylogenetic comparison of zebrafish NLRs with orthologs in tetrapods, and analysis of their tissue-specific expression. Results. Three distinct NLR subfamilies were identified by mining genome databases of various non-mammalian vertebrates; the first subfamily (NLR-A) resembles mammalian NODs, the second (NLR-B) resembles mammalian NALPs, while the third (NLR-C) appears to be unique to teleost fish. In zebrafish, NLR-A and NLR-B subfamilies contain five and six genes respectively. The third subfamily is large, containing several hundred NLR-C genes, many of which are predicted to encode a C-terminal B30.2 domain. This subfamily most likely evolved from a NOD3-like molecule. Gene predictions for zebrafish NLRs were verified using sequence derived from ESTs or direct sequencing of cDNA. Reverse-transcriptase (RT)-PCR analysis confirmed expression of representative genes from each subfamily in selected tissues. Conclusion. Our findings confirm the presence of multiple NLR gene orthologs, which form a large multigene family in teleostei. Although the functional significance of the three major NLR subfamilies is unclear, we speculate that conservation and abundance of NLR molecules in all teleostei genomes, reflects an essential role in cellular control, apoptosis or immunity throughout bony fish. ?? 2008 Laing et al; licensee BioMed Central Ltd.

  17. Molecular and evolutionary analysis of two divergent subfamilies of a novel miniature inverted repeat transposable element in the yellow fever mosquito, Aedes aegypti.

    Science.gov (United States)

    Tu, Z

    2000-09-01

    A novel family of miniature inverted repeat transposable elements (MITEs) named Pony was discovered in the yellow fever mosquito, Aedes aegypti. It has all the characteristics of MITEs, including terminal inverted repeats, no coding potential, A+T richness, small size, and the potential to form stable secondary structures. Past mobility of PONY: was indicated by the identification of two Pony insertions which resulted in the duplication of the TA dinucleotide targets. Two highly divergent subfamilies, A and B, were identified in A. aegypti based on sequence comparison and phylogenetic analysis of 38 elements. These subfamilies showed less than 62% sequence similarity. However, within each subfamily, most elements were highly conserved, and multiple subgroups could be identified, indicating recent amplifications from different source genes. Different scenarios are presented to explain the evolutionary history of these subfamilies. Both subfamilies share conserved terminal inverted repeats similar to those of the Tc2 DNA transposons in Caenorhabditis elegans, indicating that Pony may have been borrowing the transposition machinery from a Tc2-like transposon in mosquitoes. In addition to the terminal inverted repeats, full-length and partial subterminal repeats of a sequence motif TTGATTCAWATTCCGRACA represent the majority of the conservation between the two subfamilies, indicating that they may be important structural and/or functional components of the Pony elements. In contrast to known autonomous DNA transposons, both subfamilies of PONY: are highly reiterated in the A. aegypti genome (8,400 and 9, 900 copies, respectively). Together, they constitute approximately 1. 1% of the entire genome. Pony elements were frequently found near other transposable elements or in the noncoding regions of genes. The relative abundance of MITEs varies in eukaryotic genomes, which may have in part contributed to the different organizations of the genomes and reflect different types

  18. A genomic view of the NOD-like receptor family in teleost fish: identification of a novel NLR subfamily in zebrafish

    Directory of Open Access Journals (Sweden)

    Winton James R

    2008-02-01

    Full Text Available Abstract Background A large multigene family of NOD-like receptor (NLR molecules have been described in mammals and implicated in immunity and apoptosis. Little information, however, exists concerning this gene family in non-mammalian taxa. This current study, therefore, provides an in-depth investigation of this gene family in lower vertebrates including extensive phylogenetic comparison of zebrafish NLRs with orthologs in tetrapods, and analysis of their tissue-specific expression. Results Three distinct NLR subfamilies were identified by mining genome databases of various non-mammalian vertebrates; the first subfamily (NLR-A resembles mammalian NODs, the second (NLR-B resembles mammalian NALPs, while the third (NLR-C appears to be unique to teleost fish. In zebrafish, NLR-A and NLR-B subfamilies contain five and six genes respectively. The third subfamily is large, containing several hundred NLR-C genes, many of which are predicted to encode a C-terminal B30.2 domain. This subfamily most likely evolved from a NOD3-like molecule. Gene predictions for zebrafish NLRs were verified using sequence derived from ESTs or direct sequencing of cDNA. Reverse-transcriptase (RT-PCR analysis confirmed expression of representative genes from each subfamily in selected tissues. Conclusion Our findings confirm the presence of multiple NLR gene orthologs, which form a large multigene family in teleostei. Although the functional significance of the three major NLR subfamilies is unclear, we speculate that conservation and abundance of NLR molecules in all teleostei genomes, reflects an essential role in cellular control, apoptosis or immunity throughout bony fish.

  19. Generic revision of the ant subfamily Dorylinae (Hymenoptera, Formicidae)

    Science.gov (United States)

    Borowiec, Marek L.

    2016-01-01

    Abstract The generic classification of the ant subfamily Dorylinae is revised, with the aim of facilitating identification of easily-diagnosable monophyletic genera. The new classification is based on recent molecular phylogenetic evidence and a critical reappraisal of doryline morphology. New keys and diagnoses based on workers and males are provided, along with reviews of natural history and phylogenetic relationships, distribution maps, and a list of valid species for each lineage. Twenty-eight genera (27 extant and 1 extinct) are recognized within the subfamily, an increase from 20 in the previous classification scheme. Species classified in the polyphyletic Cerapachys and Sphinctomyrmex prior to this publication are here distributed among 9 and 3 different genera, respectively. Amyrmex and Asphinctanilloides are synonymized under Leptanilloides and the currently recognized subgenera are synonymized for Dorylus. No tribal classification is proposed for the subfamily, but several apparently monophyletic genus-groups are discussed. Valid generic names recognized here include: Acanthostichus (= Ctenopyga), Aenictogiton, Aenictus (= Paraenictus, Typhlatta), Cerapachys (= Ceratopachys), Cheliomyrmex, Chrysapace gen. rev., Cylindromyrmex (= Holcoponera, Hypocylindromyrmex, Metacylindromyrmex), Dorylus (= Alaopone syn. n., Anomma syn. n., Cosmaecetes, Dichthadia syn. n., Rhogmus syn. n., Shuckardia, Sphecomyrmex, Sphegomyrmex, Typhlopone syn. n.), Eburopone gen. n., Eciton (= Camptognatha, Holopone, Mayromyrmex), Eusphinctus gen. rev., Labidus (= Nycteresia, Pseudodichthadia), Leptanilloides (= Amyrmex syn. n., Asphinctanilloides syn. n.), Lioponera gen. rev. (= Neophyracaces syn. n., Phyracaces syn. n.), Lividopone, Neivamyrmex (= Acamatus, Woitkowskia), Neocerapachys gen. n., Nomamyrmex, Ooceraea gen. rev. (= Cysias syn. n.), Parasyscia gen. rev., †Procerapachys, Simopone, Sphinctomyrmex, Syscia gen. rev., Tanipone, Vicinopone, Yunodorylus gen. rev., Zasphinctus

  20. Estrous Cycle and Gestational Age-Dependent Expression of Members of the Interleukin-36 Subfamily in a Semi-Allogeneic Model of Infected and Non-Infected Murine Pregnancy

    Science.gov (United States)

    Murrieta-Coxca, José Martin; Gómez-Chávez, Fernando; Baeza-Martínez, Damariz Adriana; Cancino-Diaz, Mario Eugenio; Cancino-Diaz, Juan Carlos; Pérez-Tapia, Sonia Mayra; Reyes-Maldonado, Elba; Rodríguez-Martínez, Sandra

    2016-01-01

    The IL-36 subfamily is a recently described group of cytokines with pro-inflammatory behavior, comprising three agonists (α, β, and γ), its receptor (R), and one antagonist (Ra). The expression and function of IL-36 subfamily members in the estrous cycle in healthy and infected pregnancy has not been described. We evaluated mRNA and protein expression of IL-36 family members during the estrous cycle, implantation, fetal development, and post-labor periods in a model of allogenic pregnancy in mice. We also explored the ability of Listeria monocytogenes to modulate the expression of IL-36 subfamily members during pregnancy. Expression of IL-36 subfamily members showed different expression during the estrous cycle and pregnancy but was induced at estrous, 16.5 days post coitum (dpc), 18.5 dpc, and labor. IL-36 subfamily members showed a characteristic distribution in the glandular epithelium, perimetrium, myometrium, and stratum vasculare. Infection with L. monocytogenes during pregnancy induced strong production of IL-36 subfamily members, an observation that correlated with an increasing prevalence of fetal loss. In conclusion, IL-36 agonists showed specific patterns of mRNA and protein expression that might suggest functional specialization or specific target cells. Infection with L. monocytogenes during pregnancy induced strong production of IL-36 subfamily members. PMID:27713746

  1. Estrous cycle and gestational age-dependent expression of members of the interleukin-36 subfamily in a semi-allogeneic model of infected and non-infected murine pregnancy

    Directory of Open Access Journals (Sweden)

    José Martin Murrieta Coxca

    2016-09-01

    Full Text Available The IL-36 subfamily is a recently described group of cytokines with pro-inflammatory behavior, comprising three agonists (α, β and γ, its receptor (R and one antagonist (Ra. The expression and function of IL-36 subfamily members in the estrous cycle in healthy and infected pregnancy have not been described. We evaluated mRNA and protein expression of IL-36 family members during the estrous cycle, implantation, fetal development and post-labor periods in a model of allogenic pregnancy in mice. We also explored the ability of Listeria monocytogenes to modulate expression of IL-36 subfamily members during pregnancy. Expression of IL-36 subfamily members showed different expression during the estrous cycle and pregnancy, but was induced at estrous, 16.5 days post coitum (dpc, 18.5 dpc and labor. IL-36 subfamily members showed a characteristic distribution in the glandular epithelium, perimetrium, myometrium, and stratum vasculare. Infection with Listeria monocytogenes during pregnancy induced strong production of IL-36 subfamily members, an observation that correlated with an increasing prevalence of fetal loss. Conclusions: IL-36 agonists showed specific patterns of mRNA and protein expression that might suggest functional specialization or specific target cells. Infection with Listeria monocytogenes during pregnancy induced strong production of IL-36 subfamily members.

  2. Nonlinear interaction of intense hypergeometric Gaussian subfamily laser beams in plasma

    Science.gov (United States)

    Sobhani, H.; Vaziri (Khamedi), M.; Rooholamininejad, H.; Bahrampour, A. R.

    2016-07-01

    Propagation of Hypergeometric-Gaussian laser beam in a nonlinear plasma medium is investigated by considering the Source Dependent Expansion method. A subfamily of Hypergeometric-Gaussian beams with a non-negative, even and integer radial index, can be expressed as the linear superposition of finite number of Laguerre-Gaussian functions. Propagation of Hypergeometric-Gaussian beams in a nonlinear plasma medium depends on the value of radial index. The bright rings' number of these beams is changed during the propagation in plasma medium. The effect of beam vortex charge number l and initial (input) beam intensity on the self-focusing of Hypergeometric-Gaussian beams is explored. Also, by choosing the suitable initial conditions, Hypergeometric-Gaussian subfamily beams can be converted to one or more mode components that a typical of mode conversion may be occurred. The self-focusing of these winding beams can be used to control the focusing force and improve the electron bunch quality in laser plasma accelerators.

  3. Identification and analysis of evolutionary selection pressures acting at the molecular level in five forkhead subfamilies.

    Science.gov (United States)

    Fetterman, Christina D; Rannala, Bruce; Walter, Michael A

    2008-09-24

    Members of the forkhead gene family act as transcription regulators in biological processes including development and metabolism. The evolution of forkhead genes has not been widely examined and selection pressures at the molecular level influencing subfamily evolution and differentiation have not been explored. Here, in silico methods were used to examine selection pressures acting on the coding sequence of five multi-species FOX protein subfamily clusters; FoxA, FoxD, FoxI, FoxO and FoxP. Application of site models, which estimate overall selection pressures on individual codons throughout the phylogeny, showed that the amino acid changes observed were either neutral or under negative selection. Branch-site models, which allow estimated selection pressures along specified lineages to vary as compared to the remaining phylogeny, identified positive selection along branches leading to the FoxA3 and Protostomia clades in the FoxA cluster and the branch leading to the FoxO3 clade in the FoxO cluster. Residues that may differentiate paralogs were identified in the FoxA and FoxO clusters and residues that differentiate orthologs were identified in the FoxA cluster. Neutral amino acid changes were identified in the forkhead domain of the FoxA, FoxD and FoxP clusters while positive selection was identified in the forkhead domain of the Protostomia lineage of the FoxA cluster. A series of residues under strong negative selection adjacent to the N- and C-termini of the forkhead domain were identified in all clusters analyzed suggesting a new method for refinement of domain boundaries. Extrapolation of domains among cluster members in conjunction with selection pressure information allowed prediction of residue function in the FoxA, FoxO and FoxP clusters and exclusion of known domain function in residues of the FoxA and FoxI clusters. Consideration of selection pressures observed in conjunction with known functional information allowed prediction of residue function and

  4. Identification and analysis of evolutionary selection pressures acting at the molecular level in five forkhead subfamilies

    Directory of Open Access Journals (Sweden)

    Rannala Bruce

    2008-09-01

    Full Text Available Abstract Background Members of the forkhead gene family act as transcription regulators in biological processes including development and metabolism. The evolution of forkhead genes has not been widely examined and selection pressures at the molecular level influencing subfamily evolution and differentiation have not been explored. Here, in silico methods were used to examine selection pressures acting on the coding sequence of five multi-species FOX protein subfamily clusters; FoxA, FoxD, FoxI, FoxO and FoxP. Results Application of site models, which estimate overall selection pressures on individual codons throughout the phylogeny, showed that the amino acid changes observed were either neutral or under negative selection. Branch-site models, which allow estimated selection pressures along specified lineages to vary as compared to the remaining phylogeny, identified positive selection along branches leading to the FoxA3 and Protostomia clades in the FoxA cluster and the branch leading to the FoxO3 clade in the FoxO cluster. Residues that may differentiate paralogs were identified in the FoxA and FoxO clusters and residues that differentiate orthologs were identified in the FoxA cluster. Neutral amino acid changes were identified in the forkhead domain of the FoxA, FoxD and FoxP clusters while positive selection was identified in the forkhead domain of the Protostomia lineage of the FoxA cluster. A series of residues under strong negative selection adjacent to the N- and C-termini of the forkhead domain were identified in all clusters analyzed suggesting a new method for refinement of domain boundaries. Extrapolation of domains among cluster members in conjunction with selection pressure information allowed prediction of residue function in the FoxA, FoxO and FoxP clusters and exclusion of known domain function in residues of the FoxA and FoxI clusters. Conclusion Consideration of selection pressures observed in conjunction with known

  5. Revision of the monogenean subfamily Neothoracocotylinae Lebedev, 1969 (Polyopisthocotylea: Thoracocotylidae).

    Science.gov (United States)

    Hayward, C J; Rohde, K

    1999-11-01

    Members of the subfamily Neothoracocotylinae are gastrocotylinean monogeneans on the gills of scombrid fishes of the genera Scomberomorus and Acanthocybium, and reportedly of a coryphaenid fish belonging to the genus Coryphaena. We revise the diagnosis of the subfamily and its two genera and accept only two species as valid. Neothoracocotyle acanthocybii (Meserve, 1938) Hargis, 1956 is known from Acanthocybium solandri throughout the Pacific Ocean and in the western Atlantic. N. coryphaenae (Yamaguti, 1938) Hargis, 1956, known only from a single specimen and described from Coryphaena hippurus in Japan, is synonymised with N. acanthocybii. The sole member of Scomberocotyle, S. scomberomori (Koratha, 1955) Hargis, 1956, infects five species of Scomberomorus in the eastern Pacific Ocean and the western and castern Atlantic. We record this worm from several new hosts and/or localities, including S. sierra and S. concolor in the eastern Pacific (Mexico to Colombia), S. maculatus and S. cavalla in the western Atlantic (USA to Brazil), and S. tritor in the eastern Atlantic (Sierra Leone to Nigeria).

  6. Origin and evolution of GALA-LRR, a new member of the CC-LRR subfamily: from plants to bacteria?

    Directory of Open Access Journals (Sweden)

    Andrey V Kajava

    Full Text Available The phytopathogenic bacterium Ralstonia solanacearum encodes type III effectors, called GALA proteins, which contain F-box and LRR domains. The GALA LRRs do not perfectly fit any of the previously described LRR subfamilies. By applying protein sequence analysis and structural prediction, we clarify this ambiguous case of LRR classification and assign GALA-LRRs to CC-LRR subfamily. We demonstrate that side-by-side packing of LRRs in the 3D structures may control the limits of repeat variability within the LRR subfamilies during evolution. The LRR packing can be used as a criterion, complementing the repeat sequences, to classify newly identified LRR domains. Our phylogenetic analysis of F-box domains proposes the lateral gene transfer of bacterial GALA proteins from host plants. We also present an evolutionary scenario which can explain the transformation of the original plant LRRs into slightly different bacterial LRRs. The examination of the selective evolutionary pressure acting on GALA proteins suggests that the convex side of their horse-shoe shaped LRR domains is more prone to positive selection than the concave side, and we therefore hypothesize that the convex surface might be the site of protein binding relevant to the adaptor function of the F-box GALA proteins. This conclusion provides a strong background for further functional studies aimed at determining the role of these type III effectors in the virulence of R. solanacearum.

  7. Heterodimerization within the TREK channel subfamily produces a diverse family of highly regulated potassium channels.

    Science.gov (United States)

    Levitz, Joshua; Royal, Perrine; Comoglio, Yannick; Wdziekonski, Brigitte; Schaub, Sébastien; Clemens, Daniel M; Isacoff, Ehud Y; Sandoz, Guillaume

    2016-04-12

    Twik-related K(+) channel 1 (TREK1), TREK2, and Twik-related arachidonic-acid stimulated K(+) channel (TRAAK) form the TREK subfamily of two-pore-domain K(+) (K2P) channels. Despite sharing up to 78% sequence homology and overlapping expression profiles in the nervous system, these channels show major differences in their regulation by physiological stimuli. For instance, TREK1 is inhibited by external acidification, whereas TREK2 is activated. Here, we investigated the ability of the members of the TREK subfamily to assemble to form functional heteromeric channels with novel properties. Using single-molecule pull-down (SiMPull) from HEK cell lysate and subunit counting in the plasma membrane of living cells, we show that TREK1, TREK2, and TRAAK readily coassemble. TREK1 and TREK2 can each heterodimerize with TRAAK, but do so less efficiently than with each other. We functionally characterized the heterodimers and found that all combinations form outwardly rectifying potassium-selective channels but with variable voltage sensitivity and pH regulation. TREK1-TREK2 heterodimers show low levels of activity at physiological external pH but, unlike their corresponding homodimers, are activated by both acidic and alkaline conditions. Modeling based on recent crystal structures, along with mutational analysis, suggests that each subunit within a TREK1-TREK2 channel is regulated independently via titratable His. Finally, TREK1/TRAAK heterodimers differ in function from TRAAK homodimers in two critical ways: they are activated by both intracellular acidification and alkalinization and are regulated by the enzyme phospholipase D2. Thus, heterodimerization provides a means for diversifying functionality through an expansion of the channel types within the K2P channels.

  8. The Formation of the Polyploid Hybrids From Different Subfamily Fish Crossings and Its Evolutionary Significance

    OpenAIRE

    Liu, Shaojun; Qin, Qinbo; Xiao, Jun; Lu, Wenting; Shen, Jiamin; Li, Wei; Liu, Jifang; Duan, Wei; Zhang, Chun; Tao, De Min; Zhao, Rurong; Yan, Jinpeng; Liu, Yun

    2007-01-01

    This study provides genetic evidences at the chromosome, DNA content, DNA fragment and sequence, and morphological levels to support the successful establishment of the polyploid hybrids of red crucian carp × blunt snout bream, which belonged to a different subfamily of fish (Cyprininae subfamily and Cultrinae subfamily) in the catalog. We successfully obtained the sterile triploid hybrids and bisexual fertile tetraploid hybrids of red crucian carp (RCC) (♀) × blunt snout bream (BSB) (♂) as w...

  9. The Caenorhabditis elegans parvulin gene subfamily and their expression under cold or heat stress along with the fkb subfamily.

    Science.gov (United States)

    Fasseas, Michael K; Dimou, Maria; Katinakis, Panagiotis

    2012-07-06

    Parvulins and FKBPs are members of the peptidyl-prolyl cis/trans isomerases (PPIase) enzyme family whose role is to catalyze the interconversion between the cis trans forms of a peptide bond preceding internal proline residues in a polypeptide substrate. Members of the parvulin subfamily have been found to be involved in a variety of diseases, including Alzheimer's disease and cancer and are also considered possible antiparasitic targets. Genes Y110A2AL.13 (pin-1) and Y48C3A.16 (pin-4) were found in the worm's genome, possibly encoding parvulins. One is homologous to human and fly PIN1 whereas the other is homologous to human and fly PIN4. Both were expressed in Escherichia coli, purified and found to have in vitro PPIase activity. Expression levels of both genes, as well as the fkb genes (that encode FK506-binding proteins) were measured during development and under cold or heat stress conditions. The results revealed a potential role for these genes under temperature-related stress. RNAi silencing was performed for wild type and mutant strain worms under normal and cold or heat stress conditions. A reduced lifespan was observed when pin-4 dsRNA was fed to the fkb-5 deficient worms. Our work presents a first attempt to characterize the Caenorhabditis elegans parvulins and may present an interesting starting point for further experimentation concerning their role, along with the FKBP subfamily, in nematode physiology and their possible use as antiparasitic targets.

  10. Comprehensive Molecular Phylogeny of the Sub-Family Dipterocarpoideae (Dipterocarpaceae) Based on Chloroplast DNA Sequences

    National Research Council Canada - National Science Library

    Gamage, Dayananda Thawalama; Silva, Morley P. de; Inomata, Nobuyuki; Yamazaki, Tsuneyuki; Szmidt, Alfred E

    2006-01-01

    .... Although several previous studies addressed the phylogeny of the Dipterocarpaceae family, relationships among many of its genera from the Dipterocarpoideae sub-family are still not well understood...

  11. Two new nematode species of the subfamily Brittonematinae (Dorylaimida: Actinolaimidae

    Directory of Open Access Journals (Sweden)

    Andrássy, I.

    2010-10-01

    Full Text Available Abstract. Two new species of actinolaimoid nematodes of the subfamily Brittonematinae are described and illustrated.Actinca marisae sp. n. from Brazil is characterized by the long (on average 2.92 mm and slender body, 30–32 distinct longitudinalridges on cuticle, narrow head, slender odontostyle, onchial tips facing each other, cylindrus occupying somewhat lessthan one-half of pharynx, broad vulval lips, and by medum long tail. Afractinca eburnea sp. n. from Côte d’Ivoire can bedistinguished by a relatively long body (on average 1.88 mm, thin cuticle provided with 14 longitudinal ridges, cap-like offsetlabial ring, very slender odontostyle, long prerectum, vulva sunk in body contour, and by the elongate-conoid female tail. Mainmorphological structures of Actinca and Afractinca species are summarized. Some comments on further brittonematine speciesare added.

  12. CREB3 subfamily transcription factors are not created equal: Recent insights from global analyses and animal models

    Directory of Open Access Journals (Sweden)

    Chan Chi-Ping

    2011-02-01

    Full Text Available Abstract The CREB3 subfamily of membrane-bound bZIP transcription factors has five members in mammals known as CREB3 and CREB3L1-L4. One current model suggests that CREB3 subfamily transcription factors are similar to ATF6 in regulated intramembrane proteolysis and transcriptional activation. Particularly, they were all thought to be proteolytically activated in response to endoplasmic reticulum (ER stress to stimulate genes that are involved in unfolded protein response (UPR. Although the physiological inducers of their proteolytic activation remain to be identified, recent findings from microarray analyses, RNAi screens and gene knockouts not only demonstrated their critical roles in regulating development, metabolism, secretion, survival and tumorigenesis, but also revealed cell type-specific patterns in the activation of their target genes. Members of the CREB3 subfamily show differential activity despite their structural similarity. The spectrum of their biological function expands beyond ER stress and UPR. Further analyses are required to elucidate the mechanism of their proteolytic activation and the molecular basis of their target recognition.

  13. RINL, guanine nucleotide exchange factor Rab5-subfamily, is involved in the EphA8-degradation pathway with odin.

    Directory of Open Access Journals (Sweden)

    Hiroaki Kajiho

    Full Text Available The Rab family of small guanosine triphosphatases (GTPases plays a vital role in membrane trafficking. Its active GTP-bound state is driven by guanine nucleotide-exchange factors (GEFs. Ras and Rab interactor (or Ras interaction/interference-like (RINL, which contains a conserved VPS9 domain critical for GEF action, was recently identified as a new Rab5 subfamily GEF in vitro. However, its detailed function and interacting molecules have not yet been fully elucidated. Here we found that RINL has GEF activity for the Rab5 subfamily proteins by measuring their GTP-bound forms in cultured cells. We also found that RINL interacts with odin, a member of the ankyrin-repeat and sterile-alpha motif (SAM domain-containing (Anks protein family. In addition, the Eph tyrosine kinase receptor EphA8 formed a ternary complex with both RINL and odin. Interestingly, RINL expression in cultured cells reduced EphA8 levels in a manner dependent on both its GEF activity and interaction with odin. In addition, knockdown of RINL increased EphA8 level in HeLa cells. Our findings suggest that RINL, as a GEF for Rab5 subfamily, is implicated in the EphA8-degradation pathway via its interaction with odin.

  14. Relevant use of Klotho in FGF19 subfamily signaling system in vivo.

    Science.gov (United States)

    Tomiyama, Ken-ichi; Maeda, Ryota; Urakawa, Itaru; Yamazaki, Yuji; Tanaka, Tomohiro; Ito, Shinji; Nabeshima, Yoko; Tomita, Tsutomu; Odori, Shinji; Hosoda, Kiminori; Nakao, Kazuwa; Imura, Akihiro; Nabeshima, Yo-ichi

    2010-01-26

    Alpha-Klotho (alpha-Kl) and its homolog, beta-Klotho (beta-Kl) are key regulators of mineral homeostasis and bile acid/cholesterol metabolism, respectively. FGF15/ humanFGF19, FGF21, and FGF23, members of the FGF19 subfamily, are believed to act as circulating metabolic regulators. Analyses of functional interactions between alpha- and beta-Kl and FGF19 factors in wild-type, alpha-kl(-/-), and beta-kl(-/-) mice revealed a comprehensive regulatory scheme of mineral homeostasis involving the mutually regulated positive/negative feedback actions of alpha-Kl, FGF23, and 1,25(OH)(2)D and an analogous regulatory network composed of beta-Kl, FGF15/humanFGF19, and bile acids that regulate bile acid/cholesterol metabolism. Contrary to in vitro data, beta-Kl is not essential for FGF21 signaling in adipose tissues in vivo, because (i) FGF21 signals are transduced in the absence of beta-Kl, (ii) FGF21 could not be precipitated by beta-Kl, and (iii) essential phenotypes in Fgf21(-/-) mice (decreased expressions of Hsl and Atgl in WAT) were not replicated in beta-kl(-/-) mice. These findings suggest the existence of Klotho-independent FGF21 signaling pathway(s) where undefined cofactors are involved. One-to-one functional interactions such as alpha-Klotho/FGF23, beta-Klotho/FGF15 (humanFGF19), and undefined cofactor/FGF21 would result in tissue-specific signal transduction of the FGF19 subfamily.

  15. Whole genome identification, phylogeny and evolution of the cytochrome P450 family 2 (CYP2) sub-families in birds

    DEFF Research Database (Denmark)

    Almeida, Daniela; Maldonado, Emanuel; Khan, Imran;

    2016-01-01

    The cytochrome P450 (CYP) superfamily defends organisms from endogenous and noxious environmental compounds, and thus is crucial for survival. However, beyond mammals the molecular evolution of CYP2 subfamilies is poorly understood. Here, we characterized the CYP2 family across 48 novel avian whole......0, SRS2_SRS3 and SRS3.1) and heme binding areas that influence CYP2 structure and function of functional importance as under significant positive selection. Some of the positively selected sites in avian CYP2D are located within the same SRS1 region that was previously linked with the metabolism...

  16. On the correct name for some subfamilies of Mustelidae (Mammalia, Carnivora

    Directory of Open Access Journals (Sweden)

    Fabio Oliveira do Nascimento

    2014-01-01

    Full Text Available Mustelids (Mustelidae exhibit a wide morphological and ecological diversity, ranging from aquatic to semi arboreal and fossorial forms. It is the most diversity family in Carnivora, and this has promoted a great number of taxonomic arrangements for subfamilies, which can range from two to 15 depending on the author. The relatively recent use of molecular data has helped to elucidate the classification of mustelids, and eight subfamilies are currently recognized: Mustelinae, Galictinae, Helictidinae, Martinae, Melinae, Mellivorinae, Taxidiinae and Lutrinae. However, some of these subfamilies have nomenclatural problems, not receiving the oldest available name. The subfamily that includes martens (Martes, Charronia and Pekania, tayra (Eira and wolverine (Gulo has received the name of Martinae Wagner, 1841, but the oldest available name is Guloninae Gray, 1825. This problem also occurs for the subfamily that includes the grisons (Galictis, Patagonian weasel (Lyncodon, marbled polecat (Vormela and striped weasels (Ictonyx and Poecilogale, which are known as Grisoninae Pocock, 1921, but the correct name for this group is Ictonychinae, Pocock, 1921. The subfamily that includes ferret badgers (Melogale retains the name Helictidinae Gray, 1865, because its validity is not affected when the type-genus of the subfamily becomes a junior synonym of another genus. Furthermore, a list of the extant subfamilies of Mustelidae and their respective synonyms and included genera is provided.

  17. Historical legacies in the geographical diversity patterns of New World palm (Arecaceae) subfamilies

    DEFF Research Database (Denmark)

    Bjorholm, Stine; Svenning, Jens-Christian; Baker, William

    2006-01-01

    The extent to which species richness patterns of the major palm subfamilies in the Americas are controlled by lineage history was studied. Based on the fossil record, we suggest that the subfamily Coryphoideae has followed a boreotropical dispersal route into Central and South America, whereas ca...

  18. Phylogenetic relationships of subfamilies in the family Hesperiidae (Lepidoptera: Hesperioidea) from China.

    Science.gov (United States)

    Yuan, Xiangqun; Gao, Ke; Yuan, Feng; Wang, Ping; Zhang, Yalin

    2015-06-10

    Hesperiidae is one of the largest families of butterflies. Our knowledge of the higher systematics on hesperiids from China is still very limited. We infer the phylogenetic relationships of the subfamilies of Chinese skippers based on three mitochondrial genes (cytochrome b (Cytb), the NADH dehydrogenase subunit 1 (ND1) and cytochrome oxidase I (COI)). In this study, 30 species in 23 genera were included in the Bayesian and maximum likelihood analyses. The subfamily Coeliadinae, Eudaminae, Pyrginae and Heteropterinae were recovered as a monophyletic clade with strong support. The subfamily Hesperiinae formed a clade, but support for monophyly was weak. Our results imply that the five subfamilies of Chinese Hesperiidae should be divided into: Coeliadinae, Eudaminae, Pyrginae, Heteropterinae and Hesperiinae. The relationships of the five subfamilies should be as follows: Coeliadinae + (Eudaminae + (Pyrginae + (Heteropterinae + Hesperiinae))).

  19. The nuclear receptor gene family in the Pacific oyster, Crassostrea gigas, contains a novel subfamily group.

    Science.gov (United States)

    Vogeler, Susanne; Galloway, Tamara S; Lyons, Brett P; Bean, Tim P

    2014-05-15

    Nuclear receptors are a superfamily of transcription factors important in key biological, developmental and reproductive processes. Several of these receptors are ligand- activated and through their ability to bind endogenous and exogenous ligands, are potentially vulnerable to xenobiotics. Molluscs are key ecological species in defining aquatic and terrestrial habitats and are sensitive to xenobiotic compounds in the environment. However, the understanding of nuclear receptor presence, function and xenobiotic disruption in the phylum Mollusca is limited. Here, forty-three nuclear receptor sequences were mined from the genome of the Pacific oyster, Crassostrea gigas. They include members of NR0-NR5 subfamilies, notably lacking any NR6 members. Phylogenetic analyses of the oyster nuclear receptors have been conducted showing the presence of a large novel subfamily group not previously reported, which is named NR1P. Homologues to all previous identified nuclear receptors in other mollusc species have also been determined including the putative heterodimer partner retinoid X receptor, estrogen receptor and estrogen related receptor. C. gigas contains a highly diverse set of nuclear receptors including a novel NR1 group, which provides important information on presence and evolution of this transcription factor superfamily in invertebrates. The Pacific oyster possesses two members of NR3, the sex steroid hormone receptor analogues, of which there are 9 in humans. This provides increasing evidence that steroid ligand specific expansion of this family is deuterostome specific. This new knowledge on divergence and emergence of nuclear receptors in C. gigas provides essential information for studying regulation of molluscan gene expression and the potential effects of xenobiotics.

  20. VAMP subfamilies identified by specific R-SNARE motifs.

    Science.gov (United States)

    Rossi, Valeria; Picco, Raffaella; Vacca, Marcella; D'Esposito, Maurizio; D'Urso, Michele; Galli, Thierry; Filippini, Francesco

    2004-05-01

    In eukaryotes, interactions among the alpha-helical coiled-coil domains (CCDs) of soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs) play a pivotal role in mediating the fusion among vesicles and target membranes. Surface residues of such CCDs are major candidates to regulate the specificity of membrane fusion, as they may alter local charge at the interaction layers and surface of the fusion complex, possibly modulating its formation and/or the binding of non-SNARE regulatory factors. Based on alternate patterns in surface residues, we have identified two motifs which group vesicular SNAREs in two novel subfamilies: RG-SNAREs and RD-SNAREs. The RG-SNARE CCD is common to all members of the widely conserved family of long VAMPs or longins and to yeast and non-neuronal VAMPs, possibly mediating "basic" fusion mechanisms; instead, only synaptobrevins from Bilateria share an RD-SNARE CCD, which is likely to mediate interactions to specific, yet unknown, regulatory factors and/or be the landmark of rapid fusion reactions like that mediating the release of neurotransmitters.

  1. Phylogeny of ladybirds (Coleoptera: Coccinellidae): are the subfamilies monophyletic?

    Science.gov (United States)

    Magro, A; Lecompte, E; Magné, F; Hemptinne, J-L; Crouau-Roy, B

    2010-03-01

    The Coccinellidae (ladybirds) is a highly speciose family of the Coleoptera. Ladybirds are well known because of their use as biocontrol agents, and are the subject of many ecological studies. However, little is known about phylogenetic relationships of the Coccinellidae, and a precise evolutionary framework is needed for the family. This paper provides the first phylogenetic reconstruction of the relationships within the Coccinellidae based on analysis of five genes: the 18S and 28S rRNA nuclear genes and the mitochondrial 12S, 16S rRNA and cytochrome oxidase subunit I (COI) genes. The phylogenetic relationships of 67 terminal taxa, representative of all the subfamilies of the Coccinellidae (61 species, 37 genera), and relevant outgroups, were reconstructed using multiple approaches, including Bayesian inference with partitioning strategies. The recovered phylogenies are congruent and show that the Coccinellinae is monophyletic but the Coccidulinae, Epilachninae, Scymninae and Chilocorinae are paraphyletic. The tribe Chilocorini is identified as the sister-group of the Coccinellinae for the first time. Copyright 2009 Elsevier Inc. All rights reserved.

  2. Bacterial lipoxygenases, a new subfamily of enzymes? A phylogenetic approach.

    Science.gov (United States)

    Hansen, Jhoanne; Garreta, Albert; Benincasa, Maria; Fusté, M Carmen; Busquets, Montserrat; Manresa, Angeles

    2013-06-01

    Lipoxygenases (EC. 1.13.11.12) are a non-heme iron enzymes consisting of one polypeptide chain folded into two domains, the N-terminal domain and the catalytic moiety β-barrel domain. They catalyze the dioxygenation of 1Z,4Z-pentadiene moieties of polyunsaturated fatty acids obtaining hydroperoxy fatty acids. For years, the presence of lipoxygenases was considered a eukaryotic feature, present in mammals, plants, small marine invertebrates, and fungi, but now, some lipoxygenase sequences have been detected on prokaryotic organisms, changing the idea that lipoxygenases are exclusively a eukaryotic affair. Lipoxygenases are involved in different types of reactions on eukaryote organisms where the biological role and the structural characteristics of these enzymes are well studied. However, these aspects of the bacterial lipoxygenases have not yet been elucidated and are unknown. This revision discusses biochemical aspects, biological applications, and some characteristics of these enzymes and tries to determine the existence of a subfamily of bacterial lipoxygenases in the context of the phylogeny of prokaryotic lipoxygenases, supporting the results of phylogenetic analyzes with the comparison and discussion of structural information of the first prokaryotic lipoxygenase crystallized and other eukaryotic lipoxygenases structures.

  3. Evolution of substrate recognition sites (SRSs) in cytochromes P450 from Apiaceae exemplified by the CYP71AJ subfamily

    DEFF Research Database (Denmark)

    Dueholm, Bjørn; Krieger, Celia; Drew, Damian;

    2015-01-01

    Background: Large proliferations of cytochrome P450 encoding genes resulting from gene duplications can be termed as 'blooms', providing genetic material for the genesis and evolution of biosynthetic pathways. Furanocoumarins are allelochemicals produced by many of the species in Apiaceaous plants...... and four other subclades were identified and shown to be part of two distinct clades within the CYP71AJ subfamily. The subclades show significant variability within their substrate recognition sites between the clades, suggesting different biochemical functions and providing insights into the evolution...

  4. Protein complex interactor analysis and differential activity of KDM3 subfamily members towards H3K9 methylation.

    Directory of Open Access Journals (Sweden)

    Michael Brauchle

    Full Text Available Histone modifications play an important role in chromatin organization and gene regulation, and their interpretation is referred to as epigenetic control. The methylation levels of several lysine residues in histone tails are tightly controlled, and JmjC domain-containing proteins are one class of broadly expressed enzymes catalyzing methyl group removal. However, several JmjC proteins remain uncharacterized, gaps persist in understanding substrate recognition, and the integration of JmjC proteins into signaling pathways is just emerging. The KDM3 subfamily is an evolutionarily conserved group of histone demethylase proteins, thought to share lysine substrate specificity. Here we use a systematic approach to compare KDM3 subfamily members. We show that full-length KDM3A and KDM3B are H3K9me1/2 histone demethylases whereas we fail to observe histone demethylase activity for JMJD1C using immunocytochemical and biochemical approaches. Structure-function analyses revealed the importance of a single amino acid in KDM3A implicated in the catalytic activity towards H3K9me1/2 that is not conserved in JMJD1C. Moreover, we use quantitative proteomic analyses to identify subsets of the interactomes of the 3 proteins. Specific interactor candidates were identified for each of the three KDM3 subfamily members. Importantly, we find that SCAI, a known transcriptional repressor, interacts specifically with KDM3B. Taken together, we identify substantial differences in the biology of KDM3 histone demethylases, namely enzymatic activity and protein-protein interactions. Such comparative approaches pave the way to a better understanding of histone demethylase specificity and protein function at a systems level and are instrumental in identifying the more subtle differences between closely related proteins.

  5. Characteristics of bryophytes with gemmae from a karst bauxite mine:A case study of Lindai mine in Zhanj ie town,Qingzhen,Guizhou%贵州喀斯特铝土矿具芽胞苔藓种类特征--以贵州省清镇市林歹铝土矿区为例

    Institute of Scientific and Technical Information of China (English)

    殷声锋; 王智慧; 张朝晖

    2014-01-01

    对贵州省清镇市站街镇林歹铝土矿第二矿区的油菜种植区、矿土上部树林区、废石堆积区、矿土堆积恢复区4类环境进行苔藓植物采集,并对具芽胞苔藓种类进行统计分析,结果表明:(1)经鉴定发现苔藓植物10科22属37种,优势种(频度大于10%)为日本大丛藓Molendoajaponica Broth.(18.72%)和银叶真藓Bryumargenteum Hedw.(11.06%);(2)发现8种具芽胞苔藓,占总种数的21.62%,隶属于丛藓科 Pottiaceae 和真藓科 Bryaceae,其中日本大丛藓和芽胞银藓Anomobryumgemmigerum Broth.为常见具芽胞苔藓;(3)油菜种植区中具芽胞苔藓种类最多(6种),但出现频度不高,非该类环境中的优势种,日本大丛藓在 4类环境中均有发现;(4)在 4类环境中,相对恶劣条件下具芽胞苔藓出现的几率更大;(5)瘤根真藓 Bryum bornholmense Winkelm.& Ruthe.和毛状真藓 Bryum apiculatum Schwagr.的芽胞长于假根上,其余种类芽胞均见于叶腋处,呈扫帚状,芽胞形态上呈现多样性,有球形、棒形、棒槌形、芽形、纺锤状和火炬状。%Bryophytes were collected from four different habitats in Lindai #2 bauxite mine in Zhanjie town, Qingzhen City,Guizhou Province,and the bryophytes with gemmae were statistically analyzed.The result showed that,(1)120 samples were collected from sampling sites,and 10 families,22 genera and 37 species were identified.The dominant species (frequency >10%)were Molendoa japonica Broth (18.72%)and Bryumargenteum Hedw.(11.06%).(2)8 kinds of bryophytes had gemmae,which were attached to Potti-aceae and Bryaceae,accounting for 21.62% of the total.Of these,Molendoajaponica Broth and Bryumar-genteum Hedw.were common bryophytes with gemmae,found in 44 samples and 16 samples respectively. (3)The largest quantities of bryophytes with gemmae were found in areas where rape was cultivated (6 spe-cies);however,frequency was low and there was no dominant species.Additionally,Molendoa japonica Broth

  6. A faunistic study on some subfamilies of Braconidae (Hymenoptera: Ichneumonoidea) from Iran

    NARCIS (Netherlands)

    Samin, N.; Achterberg, van C.; Erdoğan, Ö. Ç.

    2016-01-01

    This paper deals with the species of Braconidae (Hymenoptera: Ichneumonoidea) recently collected in 13 provinces of Iran. In total, 33 species belonging to 16 subfamilies: Charmontinae, Cheloninae, Doryctinae, Euphorinae, Exothecinae, Histeromerinae, Homolobinae, Ichneutinae, Macrocentrinae, Microty

  7. Analysis of the features and source gene composition of the AluYg6 subfamily of human retrotransposons

    Directory of Open Access Journals (Sweden)

    Brookfield John FY

    2007-07-01

    Full Text Available Abstract Background Alu elements are a family of SINE retrotransposons in primates. They are classified into subfamilies according to specific diagnostic mutations from the general Alu consensus. It is now believed that there may be several retrotranspositionally-competent source genes within an Alu subfamily. To investigate the evolution of young Alu elements it is critical to have access to complete subfamilies, which, following the release of the final human genome assembly, can now be obtained using in silico methods. Results 380 elements belonging to the young AluYg6 subfamily were identified in the human genome, a number significantly exceeding prior expectations. An AluYg6 element was also identified in the chimpanzee genome, indicating that the subfamily is older than previously estimated, and appears to have undergone a period of dormancy before its expansion. The relative contributions of back mutation and gene conversion to variation at the six diagnostic positions are examined, and cases of complete forward gene conversion events are reported. Two small subfamilies derived from AluYg6 have been identified, named AluYg6a2 and AluYg5b3, which contain 40 and 27 members, respectively. These small subfamilies are used to illustrate the ambiguity regarding Alu subfamily definition, and to assess the contribution of secondary source genes to the AluYg6 subfamily. Conclusion The number of elements in the AluYg6 subfamily greatly exceeds prior expectations, indicating that the current knowledge of young Alu subfamilies is incomplete, and that prior analyses that have been carried out using these data may have generated inaccurate results. A definition of primary and secondary source genes has been provided, and it has been shown that several source genes have contributed to the proliferation of the AluYg6 subfamily. Access to the sequence data for the complete AluYg6 subfamily will be invaluable in future computational analyses investigating

  8. Adaptive evolution after gene duplication in alpha-KT x 14 subfamily from Buthus martensii Karsch.

    Science.gov (United States)

    Cao, Zhijian; Mao, Xin; Xu, Xiuling; Sheng, Jiqun; Dai, Chao; Wu, Yingliang; Luo, Feng; Sha, Yonggang; Jiang, Dahe; Li, Wenxin

    2005-07-01

    A series of isoforms of alpha-KT x 14 (short chain potassium channel scorpion toxins) were isolated from the venom of Buthus martensii Karsch by RACE and screening cDNA library methods. These isoforms adding BmKK1--3 and BmSKTx1--2 together shared high homology (more than 97%) with each other. The result of genomic sequence analysis showed that a length 79 bp intron is inserted Ala codes between the first and the second base at the 17th amino acid of signal peptide. The introns of these isoforms also share high homology with those of BmKK2 and BmSKT x 1 reported previously. Sequence analysis of many clones of cDNA and genomic DNA showed that a species population or individual polymorphism of alpha-KT x 14 genes took place in scorpion Buthus martensii Karsch and accelerated evolution played an important role in the forming process of alpha-KT x 14 scorpion toxins subfamily. The result of southern hybridization indicated that alpha-KT x 14 toxin genes existed in scorpion chromosome with multicopies. All findings maybe provided an important evidence for an extensive evolutionary process of the scorpion "pharmacological factory": at the early course of evolution, the ancestor toxic gene duplicated into a series of multicopy genes integrated at the different chromosome; at the late course of evolution, subsequent functional divergence of duplicate genes was generated by mutations, deletions and insertion.

  9. The discovery of phiAGATE, a novel phage infecting Bacillus pumilus, leads to new insights into the phylogeny of the subfamily Spounavirinae.

    Directory of Open Access Journals (Sweden)

    Jakub Barylski

    Full Text Available The Bacillus phage phiAGATE is a novel myovirus isolated from the waters of Lake Góreckie (a eutrophic lake in western Poland. The bacteriophage infects Bacillus pumilus, a bacterium commonly observed in the mentioned reservoir. Analysis of the phiAGATE genome (149844 base pairs resulted in 204 predicted protein-coding sequences (CDSs, of which 53 could be functionally annotated. Further investigation revealed that the bacteriophage is a member of a previously undescribed cluster of phages (for the purposes of this study we refer to it as "Bastille group" within the Spounavirinae subfamily. Here we demonstrate that these viruses constitute a distinct branch of the Spounavirinae phylogenetic tree, with limited similarity to phages from the Twortlikevirus and Spounalikevirus genera. The classification of phages from the Bastille group into any currently accepted genus proved extremely difficult, prompting concerns about the validity of the present taxonomic arrangement of the subfamily.

  10. Datziinae as a new subfamily name for the unavailable name Protopsychodinae Stebner et al., 2015, (Diptera: Psychodidae

    Directory of Open Access Journals (Sweden)

    Frauke Stebner

    2015-11-01

    Full Text Available In a recent paper a new subfamily of Psychodidae was inadequately named Protopsychodinae. This nomenclatural act cannot be considered as a valid name under ICZN regulations because the subfamily name is not based on the type genus Datzia Stebner et al., 2015, and furthermore the fossil genus Protopsychoda Azar et al., 1999 was originally described under the subfamily Psychodinae. Therefore, the new family-group name Datziinae is herein proposed.

  11. Phantoms of Gondwana?-phylogeny of the spider subfamily Mynogleninae (Araneae: Linyphiidae)

    DEFF Research Database (Denmark)

    Frick, Holger; Scharff, Nikolaj

    2014-01-01

    and Micronetini), and Erigoninae, and a representative of the family Pimoidae, the sister-group to Linyphiidae. No fewer than 147 of the morphological characters used in this study are new and defined for this study, and come mainly from male and female genitalia. Parsimony analysis with equal weights resulted......This is the first genus-level phylogeny of the subfamily Mynogleninae. It is based on 190 morphological characters scored for 44 taxa: 37 mynoglenine taxa (ingroup) representing 15 of the 17 known genera and seven outgroup taxa representing the subfamilies Stemonyphantinae, Linyphiinae (Linyphiini...... in three most parsimonious trees of length 871. The monophyly of the subfamily Mynogleninae and the genera Novafroneta, Parafroneta, Laminafroneta, Afroneta, Promynoglenes, Metamynoglenes, and Haplinis are supported, whereas Pseudafroneta is paraphyletic. The remaining seven mynoglenine genera are either...

  12. Nine novel microsatellite markers for the army ant Simopelta pergandei (subfamily Ponerinae)

    DEFF Research Database (Denmark)

    Kronauer, D.J.C.; Boomsma, J.J.; Pierce, N.E.

    2011-01-01

    Simopelta (subfamily Ponerinae) army ants are specialized predators of other ants in New World tropical forests. Although they show a striking convergence in overall life-history with the well known army ants of the subfamilies Aenictinae, Dorylinae, and Ecitoninae, the genus has been little.......0) and expected heterozygosities between 0.32 and 0.85 (mean: 0.65). These genetic markers will be useful in studying the sociobiology and molecular ecology of Simopelta army ants and in elucidating convergent evolutionary trajectories that have culminated in the army ant lifestyle...

  13. A new subfamily of the grasshopper (Orthoptera: Acridoidea:Gomphoceridae) from the Tibetan Plateau of China

    Institute of Scientific and Technical Information of China (English)

    Dao-Chuan Zhang; Yu-Long Zhang; Xiang-Chu Yin

    2012-01-01

    This paper reports a new subfamily,a new genus and a new species,that is,Pacrinae subfam.nov.,Pacris gen.nov and Pacris xizangensis sp.nov in Gomphoceridae.The new subfamily is allied to Orinhippinae of Gomphoceridae and it differs from the latter by wings and tympanum absent.The new genus is similar to Orinhippus Uvarov,1921 but differs from the latter in: (i) foveolae absent; (ii) tegmina absent; (iii) tympanum absent;(iv) hind margin ofpronotum with incised in the middle.Type specimens are deposited in the Museum of Hebei University,Baoding,China.

  14. Phylogenetic analysis and expression patterns of Pax genes in the onychophoran Euperipatoides rowelli reveal a novel bilaterian Pax subfamily.

    Science.gov (United States)

    Franke, Franziska Anni; Schumann, Isabell; Hering, Lars; Mayer, Georg

    2015-01-01

    Pax family genes encode a class of transcription factors that regulate various developmental processes. To shed light on the evolutionary history of these genes in Panarthropoda (Onychophora + Tardigrada + Arthropoda), we analyzed the Pax repertoire in the embryonic and adult transcriptomes of the onychophoran Euperipatoides rowelli. Our data revealed homologs of all five major bilaterian Pax subfamilies in this species, including Pax2/5/8, Pax4/6, Pox-neuro, Pax1/9/Pox-meso, and Pax3/7. In addition, we identified a new Pax member, pax-α, which does not fall into any other known Pax subfamily but instead clusters in the heterogenic Pax-α/β clade containing deuterostome, ecdysozoan, and lophotrochozoan gene sequences. These findings suggest that the last common bilaterian ancestor possessed six rather than five Pax genes, which have been retained in the panarthropod lineage. The expression data of Pax orthologs in the onychophoran embryo revealed distinctive patterns, some of which might be related to their ancestral roles in the last common panarthropod ancestor, whereas others might be specific to the onychophoran lineage. The derived roles include, for example, an involvement of pax2/5/8, pox-neuro, and pax3/7 in onychophoran nephridiogenesis, and an additional function of pax2/5/8 in the formation of the ventral and preventral organs. Furthermore, our transcriptomic analyses suggest that at least some Pax genes, including pax6 and pax-α, are expressed in the adult onychophoran head, although the corresponding functions remain to be clarified. The remarkable diversity of the Pax expression patterns highlights the functional and evolutionary plasticity of these genes in panarthropods.

  15. Comparative analysis of serine/arginine-rich proteins across 27 eukaryotes: insights into sub-family classification and extent of alternative splicing.

    Directory of Open Access Journals (Sweden)

    Dale N Richardson

    Full Text Available Alternative splicing (AS of pre-mRNA is a fundamental molecular process that generates diversity in the transcriptome and proteome of eukaryotic organisms. SR proteins, a family of splicing regulators with one or two RNA recognition motifs (RRMs at the N-terminus and an arg/ser-rich domain at the C-terminus, function in both constitutive and alternative splicing. We identified SR proteins in 27 eukaryotic species, which include plants, animals, fungi and "basal" eukaryotes that lie outside of these lineages. Using RNA recognition motifs (RRMs as a phylogenetic marker, we classified 272 SR genes into robust sub-families. The SR gene family can be split into five major groupings, which can be further separated into 11 distinct sub-families. Most flowering plants have double or nearly double the number of SR genes found in vertebrates. The majority of plant SR genes are under purifying selection. Moreover, in all paralogous SR genes in Arabidopsis, rice, soybean and maize, one of the two paralogs is preferentially expressed throughout plant development. We also assessed the extent of AS in SR genes based on a splice graph approach (http://combi.cs.colostate.edu/as/gmap_SRgenes. AS of SR genes is a widespread phenomenon throughout multiple lineages, with alternative 3' or 5' splicing events being the most prominent type of event. However, plant-enriched sub-families have 57%-88% of their SR genes experiencing some type of AS compared to the 40%-54% seen in other sub-families. The SR gene family is pervasive throughout multiple eukaryotic lineages, conserved in sequence and domain organization, but differs in gene number across lineages with an abundance of SR genes in flowering plants. The higher number of alternatively spliced SR genes in plants emphasizes the importance of AS in generating splice variants in these organisms.

  16. Phylogenetic characterization and promoter expression analysis of a novel hybrid protein disulfide isomerase/cargo receptor subfamily unique to plants and chromalveolates.

    Science.gov (United States)

    Yuen, Christen Y L; Wong, Katharine; Christopher, David A

    2016-02-01

    Protein disulfide isomerases (PDIs) play critical roles in protein folding by catalyzing the formation and rearrangement of disulfide bonds in nascent secretory proteins. There are six distinct PDI subfamilies in terrestrial plants. A unique feature of PDI-C subfamily members is their homology to the yeast retrograde (Golgi-to-endoplasmic reticulum) cargo receptor proteins, Erv41p and Erv46p. Here, we demonstrate that plant Erv41p/Erv46p-like proteins are divided into three subfamilies: ERV-A, ERV-B and PDI-C, which all possess the N-proximal and C-proximal conserved domains of yeast Erv41p and Erv46p. However, in PDI-C isoforms, these domains are separated by a thioredoxin domain. The distribution of PDI-C isoforms among eukaryotes indicates that the PDI-C subfamily likely arose through an ancient exon-shuffling event that occurred before the divergence of plants from stramenopiles and rhizarians. Arabidopsis has three PDI-C genes: PDI7, PDI12, and PDI13. PDI12- and PDI13-promoter: β-glucuronidase (GUS) gene fusions are co-expressed in pollen and stipules, while PDI7 is distinctly expressed in the style, hydathodes, and leaf vasculature. The PDI-C thioredoxin domain active site motif CxxS is evolutionarily conserved among land plants. Whereas PDI12 and PDI13 retain the CxxS motif, PDI7 has a CxxC motif similar to classical PDIs. We hypothesize that PDI12 and PDI13 maintain the ancestral roles of PDI-C in Arabidopsis, while PDI7 has undergone neofunctionalization. The unusual PDI/cargo receptor hybrid arrangement in PDI-C isoforms has no counterpart in animals or yeast, and predicts the need for pairing redox functions with cargo receptor processes during protein trafficking in plants and other PDI-C containing organisms.

  17. The structure of SAV1646 from Staphylococcus aureus belonging to a new `ribosome-associated' subfamily of bacterial proteins.

    Science.gov (United States)

    Chirgadze, Yuri N; Clarke, Teresa E; Romanov, Vladimir; Kisselman, Gera; Wu-Brown, Jean; Soloveychik, Maria; Chan, Tiffany S Y; Gordon, Roni D; Battaile, Kevin P; Pai, Emil F; Chirgadze, Nickolay Y

    2015-02-01

    The crystal structure of the SAV1646 protein from the pathogenic microorganism Staphylococcus aureus has been determined at 1.7 Å resolution. The 106-amino-acid protein forms a two-layer sandwich with α/β topology. The protein molecules associate as dimers in the crystal and in solution, with the monomers related by a pseudo-twofold rotation axis. A sequence-homology search identified the protein as a member of a new subfamily of yet uncharacterized bacterial `ribosome-associated' proteins with at least 13 members to date. A detailed analysis of the crystal protein structure along with the genomic structure of the operon containing the sav1646 gene allowed a tentative functional model of this protein to be proposed. The SAV1646 dimer is assumed to form a complex with ribosomal proteins L21 and L27 which could help to complete the assembly of the large subunit of the ribosome.

  18. Generic revision of the subfamily Betylobraconinae (Hymenoptera: Braconidae) and other groups with modified fore tarsus

    NARCIS (Netherlands)

    Achterberg, van C.

    1995-01-01

    The genera of the subfamilies Betylobraconinae, Hormiinae, Lysiterminae, Pambolinae-Chremylini, and Doryctinae-Ypsistocerini are revised. A key is given to the genera of groups belonging to the cyclostome grade including species with shortened and/or (partly) widened fore tarsus. Sixteen new genera

  19. A new genus and subgenus of the subfamily Euphorinae (Hymenoptera: Braconidae) from East Asia

    NARCIS (Netherlands)

    Belokobylskij, S.A.

    1999-01-01

    Three new taxa belonging to the subfamily Euphorinae Foerster (Hymenoptera; Braconidae) are described and illustrated. Mama mariae gen. nov. & spec. nov. from southern Far East Russia and two species of the subgenus Chaetocentistes nov. of the genus Centistes Haliday. A key to species (i.e.

  20. Classification of leaf beetles from Korea. Part V. Subfamily Megalopodinae (Coleoptera: Chrysomelidae)

    OpenAIRE

    Seung Lak An

    2015-01-01

    Korean members of the subfamily Megalopodinae are redescribed; three species are recognized, among which Temnaspis bonneuili Pic is reported for the first time in Korea. Keys, diagnoses, collection locations (domestic), distributions, host plants, and biological information about all known species are provided.

  1. Classification of leaf beetles from Korea. Part V. Subfamily Megalopodinae (Coleoptera: Chrysomelidae

    Directory of Open Access Journals (Sweden)

    Seung Lak An

    2015-12-01

    Full Text Available Korean members of the subfamily Megalopodinae are redescribed; three species are recognized, among which Temnaspis bonneuili Pic is reported for the first time in Korea. Keys, diagnoses, collection locations (domestic, distributions, host plants, and biological information about all known species are provided.

  2. Four new species of the subfamily Psilodercinae (Araneae: Ochyroceratidae) from Southwest China.

    Science.gov (United States)

    Wang, Chunxia; Li, Shuqiang

    2013-01-01

    Four new species of the family Ochyroceratidae are described from Southwest China: Althepus christae sp. nov., Lecler- cera undulatus sp. nov., Psiloderces incomptus sp. nov. from Yunnan; and P. exilis sp. nov. from Guangxi. The four spe- cies belong to the subfamily Psilodercinae.

  3. Seed morphology and anatomy and its utility in recognizing subfamilies and tribes of Zingiberaceae

    Energy Technology Data Exchange (ETDEWEB)

    Benedict, John C.; Smith, Selena Y.; Collinson, Margaret E.; Leong-Skornickova, Jana; Specht, Chelsea D.; Marone, Federica; Xiao, Xianghui; Parkinson, Dilworth Y.

    2015-11-01

    PREMISE OF THE STUDY: Recent phylogenetic analyses based on molecular data suggested that the monocot family Zingiberaceae be separated into four subfamilies and four tribes. Robust morphological characters to support these clades are lacking. Seeds were analyzed in a phylogenetic context to test independently the circumscription of clades and to better understand evolution of seed characters within Zingiberaceae. METHODS: Seventy-five species from three of the four subfamilies were analyzed using synchrotron based x-ray tomographic microscopy (SRXTM) and scored for 39 morphoanatomical characters. KEY RESULTS: Zingiberaceae seeds are some of the most structurally complex seeds in angiosperms. No single seed character was found to distinguish each subfamily, but combinations of characters were found to differentiate between the subfamilies. Recognition of the tribes based on seeds was possible for Globbeae, but not for Alpinieae, Riedelieae, or Zingibereae, due to considerable variation. CONCLUSIONS: SRXTM is an excellent, nondestructive tool to capture morphoanatomical variation of seeds and allows for the study of taxa with limited material available. Alpinioideae, Siphonochiloideae, Tamijioideae, and Zingiberoideae are well supported based on both molecular and morphological data, including multiple seed characters. Globbeae are well supported as a distinctive tribe within the Zingiberoideae, but no other tribe could be differentiated using seeds due to considerable homoplasy when compared with currently accepted relationships based on molecular data. Novel seed characters suggest tribal affinities for two currently unplaced Zingiberaceae taxa: Siliquamomum may be related to Riedelieae and Monolophus to Zingibereae, but further work is needed before formal revision of the family.

  4. New Drosophila P-like elements and reclassification of Drosophila P-elements subfamilies.

    Science.gov (United States)

    Loreto, Elgion L S; Zambra, Francis M B; Ortiz, Mauro F; Robe, Lizandra J

    2012-07-01

    Genomic searches for P-like transposable elements were performed (1) in silico in the 12 available Drosophila genomes and (2) by PCR using degenerate primers in 21 Neotropical Drosophila species. In silico searches revealed P-like sequences only in Drosophila persimilis and Drosophila willistoni. Sixteen new P-like elements were obtained by PCR. These sequences were added to sequences of previously described P-like elements, and a phylogenetic analysis was performed. The subfamilies of P-elements described in the literature (Canonical, M, O, T, and K) were included in the reconstructed tree, and all were monophyletic. However, we suggest that some subfamilies can be enlarged, other subdivided, and some new subfamilies may be proposed, totalizing eleven subfamilies, most of which contain new P-like sequences. Our analyses support the monophyly of P-like elements in Drosophilidae. We suggest that, once these elements need host-specific factors to be mobilizable, the horizontal transfer (HT) of P-like elements may be inhibited among more distant taxa. Nevertheless, HT among Drosophilidae species appears to be a common phenomenon.

  5. Wood anatomy of the Euphorbiaceae, in particular of the subfamily Phyllanthoideae

    NARCIS (Netherlands)

    Mennega, Alberta M.W.

    1985-01-01

    The great variety in wood structure of the large family Euphorbiaceae makes it impossible to describe briefly a general wood pattern. Nevertheless, a more or less clear division into four anatomical groups can be made. A short overview is given of the wood structure of the uni-ovulate subfamilies

  6. Leaf and Stem CO2 Uptake in the Three Subfamilies of the Cactaceae 1

    Science.gov (United States)

    Nobel, Park S.; Hartsock, Terry L.

    1986-01-01

    Net CO2 uptake over 24-hour periods was examined for the leaves and for the stems of 11 species of cacti representing all three subfamilies. For Pereskia aculeata, Pereskia grandifolia, and Maihuenia poeppigii (subfamily Pereskioideae), all the net shoot CO2 uptake was by the leaves and during the daytime. In contrast, for the leafless species Carnegiea gigantea, Ferocactus acanthodes, Coryphantha vivipara, and Mammillaria dioica (subfamily Cactoideae), all the shoot net CO2 uptake was by the stems and at night. Similarly, for leafless Opuntia ficus-indica (subfamily Opuntioideae), all net CO2 uptake occurred at night. For leafy members of the Opuntioideae (Pereskiopsis porteri, Quiabentia chacoensis, Austrocylindropuntia subulata), at least 88% of the shoot CO2 uptake over 24 hours was by the leaves and some CO2 uptake occurred at night. Leaves responded to the instantaneous level of photosynthetically active radiation (PAR) during the daytime, as occurs for C3 plants, whereas nocturnal CO2 uptake by stems of O. ficus-indica and F. acanthodes responded to the total daily PAR, as occurs for Crassulacean acid metabolism (CAM) plants. Thus, under the well-watered conditions employed, the Pereskioideae behaved as C3 plants, the Cactoideae behaved as CAM plants, and the Opuntioideae exhibited characteristics of both pathways. PMID:16664741

  7. New taxa of the subfamily Doryctinae Foerster (Hymenoptera: Braconidae) from French Guiana and Brazil

    NARCIS (Netherlands)

    Braet, Y.; Achterberg, van C.

    2001-01-01

    Three genera of the subfamily Doryctinae Foerster, 1862 (Hymenoptera: Braconidae) are treated and keyed: Ptesimogaster Marsh, 1965, Caingangia Marsh, 1993, and Leptodoryctes Barbalho & Penteado- Dias, 1999. The latter genus is characterised by the presence of an apical setal comb on the hind tibia.

  8. A new genus and subgenus of the subfamily Euphorinae (Hymenoptera: Braconidae) from East Asia

    NARCIS (Netherlands)

    Belokobylskij, S.A.

    1999-01-01

    Three new taxa belonging to the subfamily Euphorinae Foerster (Hymenoptera; Braconidae) are described and illustrated. Mama mariae gen. nov. & spec. nov. from southern Far East Russia and two species of the subgenus Chaetocentistes nov. of the genus Centistes Haliday. A key to species (i.e. Centiste

  9. Wood anatomy of the Euphorbiaceae, in particular of the subfamily Phyllanthoideae

    NARCIS (Netherlands)

    Mennega, Alberta M.W.

    1985-01-01

    The great variety in wood structure of the large family Euphorbiaceae makes it impossible to describe briefly a general wood pattern. Nevertheless, a more or less clear division into four anatomical groups can be made. A short overview is given of the wood structure of the uni-ovulate subfamilies Ac

  10. Leaf and Stem CO(2) Uptake in the Three Subfamilies of the Cactaceae.

    Science.gov (United States)

    Nobel, P S; Hartsock, T L

    1986-04-01

    Net CO(2) uptake over 24-hour periods was examined for the leaves and for the stems of 11 species of cacti representing all three subfamilies. For Pereskia aculeata, Pereskia grandifolia, and Maihuenia poeppigii (subfamily Pereskioideae), all the net shoot CO(2) uptake was by the leaves and during the daytime. In contrast, for the leafless species Carnegiea gigantea, Ferocactus acanthodes, Coryphantha vivipara, and Mammillaria dioica (subfamily Cactoideae), all the shoot net CO(2) uptake was by the stems and at night. Similarly, for leafless Opuntia ficus-indica (subfamily Opuntioideae), all net CO(2) uptake occurred at night. For leafy members of the Opuntioideae (Pereskiopsis porteri, Quiabentia chacoensis, Austrocylindropuntia subulata), at least 88% of the shoot CO(2) uptake over 24 hours was by the leaves and some CO(2) uptake occurred at night. Leaves responded to the instantaneous level of photosynthetically active radiation (PAR) during the daytime, as occurs for C(3) plants, whereas nocturnal CO(2) uptake by stems of O. ficus-indica and F. acanthodes responded to the total daily PAR, as occurs for Crassulacean acid metabolism (CAM) plants. Thus, under the well-watered conditions employed, the Pereskioideae behaved as C(3) plants, the Cactoideae behaved as CAM plants, and the Opuntioideae exhibited characteristics of both pathways.

  11. NR-2L: a two-level predictor for identifying nuclear receptor subfamilies based on sequence-derived features.

    Directory of Open Access Journals (Sweden)

    Pu Wang

    Full Text Available Nuclear receptors (NRs are one of the most abundant classes of transcriptional regulators in animals. They regulate diverse functions, such as homeostasis, reproduction, development and metabolism. Therefore, NRs are a very important target for drug development. Nuclear receptors form a superfamily of phylogenetically related proteins and have been subdivided into different subfamilies due to their domain diversity. In this study, a two-level predictor, called NR-2L, was developed that can be used to identify a query protein as a nuclear receptor or not based on its sequence information alone; if it is, the prediction will be automatically continued to further identify it among the following seven subfamilies: (1 thyroid hormone like (NR1, (2 HNF4-like (NR2, (3 estrogen like, (4 nerve growth factor IB-like (NR4, (5 fushi tarazu-F1 like (NR5, (6 germ cell nuclear factor like (NR6, and (7 knirps like (NR0. The identification was made by the Fuzzy K nearest neighbor (FK-NN classifier based on the pseudo amino acid composition formed by incorporating various physicochemical and statistical features derived from the protein sequences, such as amino acid composition, dipeptide composition, complexity factor, and low-frequency Fourier spectrum components. As a demonstration, it was shown through some benchmark datasets derived from the NucleaRDB and UniProt with low redundancy that the overall success rates achieved by the jackknife test were about 93% and 89% in the first and second level, respectively. The high success rates indicate that the novel two-level predictor can be a useful vehicle for identifying NRs and their subfamilies. As a user-friendly web server, NR-2L is freely accessible at either http://icpr.jci.edu.cn/bioinfo/NR2L or http://www.jci-bioinfo.cn/NR2L. Each job submitted to NR-2L can contain up to 500 query protein sequences and be finished in less than 2 minutes. The less the number of query proteins is, the shorter the time will

  12. NR-2L: a two-level predictor for identifying nuclear receptor subfamilies based on sequence-derived features.

    Science.gov (United States)

    Wang, Pu; Xiao, Xuan; Chou, Kuo-Chen

    2011-01-01

    Nuclear receptors (NRs) are one of the most abundant classes of transcriptional regulators in animals. They regulate diverse functions, such as homeostasis, reproduction, development and metabolism. Therefore, NRs are a very important target for drug development. Nuclear receptors form a superfamily of phylogenetically related proteins and have been subdivided into different subfamilies due to their domain diversity. In this study, a two-level predictor, called NR-2L, was developed that can be used to identify a query protein as a nuclear receptor or not based on its sequence information alone; if it is, the prediction will be automatically continued to further identify it among the following seven subfamilies: (1) thyroid hormone like (NR1), (2) HNF4-like (NR2), (3) estrogen like, (4) nerve growth factor IB-like (NR4), (5) fushi tarazu-F1 like (NR5), (6) germ cell nuclear factor like (NR6), and (7) knirps like (NR0). The identification was made by the Fuzzy K nearest neighbor (FK-NN) classifier based on the pseudo amino acid composition formed by incorporating various physicochemical and statistical features derived from the protein sequences, such as amino acid composition, dipeptide composition, complexity factor, and low-frequency Fourier spectrum components. As a demonstration, it was shown through some benchmark datasets derived from the NucleaRDB and UniProt with low redundancy that the overall success rates achieved by the jackknife test were about 93% and 89% in the first and second level, respectively. The high success rates indicate that the novel two-level predictor can be a useful vehicle for identifying NRs and their subfamilies. As a user-friendly web server, NR-2L is freely accessible at either http://icpr.jci.edu.cn/bioinfo/NR2L or http://www.jci-bioinfo.cn/NR2L. Each job submitted to NR-2L can contain up to 500 query protein sequences and be finished in less than 2 minutes. The less the number of query proteins is, the shorter the time will

  13. Diversity of CD2 subfamily receptors in cyprinid fishes.

    Science.gov (United States)

    Sameshima, Shiro; Nakao, Miki; Somamoto, Tomonori

    2012-01-01

    CD2 family receptor (CD2f) is evolutionarily conserved and is widely expressed by various types of leukocytes. To elucidate the phylogenetic diversity of the CD2f, we characterized CD2f in teleosts using ginbuna crucian carp and zebrafish. The identified CD2f isoforms of the ginbuna carp (caauCD2f) exhibited high sequence similarity to the mammalian CD2 subsets CD48, CD244, and CD319, but it was difficult to classify them into their respective mammalian CD2f based on sequence similarity, the presence of an immunoreceptor tyrosine-based switch motif (ITSM), and phylogenetic tree analysis. Although the four caauCD2f isoforms share an extracellular domain with quite high identity (83-94% identity at the nucleic acid level), they differ in the number of ITSM motifs in their cytoplasmic tail. RT-PCR and in situ hybridization analyses showed that the caauCD2f isoforms are expressed by different cell populations, suggesting that they, like mammalian CD2f, have diverse roles. Interestingly, immunoglobulin (Ig) domain-like sequences with high identity to caauCD2fs are clustered close together within 0.6 Mbp on zebrafish chromosomes 1 and 2 (at least 8 and 35 sequences, respectively), and many pairs of the Ig domains share more than 90% identity at the amino acid level. Therefore, the teleost CD2fs with considerably high identity have been probably generated from a common ancestral Ig-domain gene by a very recent gene duplication event. These findings suggest that the identified CD2f acquired functional diversification through successive duplications together with the acquisition of ITSM.

  14. ATP-binding cassette subfamily B member 1 (ABCB1) and subfamily C member 10 (ABCC10) are not primary resistance factors for cabazitaxel

    Institute of Scientific and Technical Information of China (English)

    Rishil J Kathawala; Yi-Jun Wang; Suneet Shukla; Yun-Kai Zhang; Saeed Alqahtani; Amal Kaddoumi; Suresh V Ambudkar; Charles R Ashby Jr; Zhe-Sheng Chen

    2015-01-01

    Introduction:ATP-binding cassette subfamily B member 1 (ABCB1) and subfamily C member 10 (ABCC10) proteins are efflux transporters that couple the energy derived from ATP hydrolysis to the translocation of toxic substances and chemotherapeutic drugs out of cells. Cabazitaxel is a novel taxane that differs from paclitaxel by its lower affinity for ATP-binding cassette (ABC) transporters. Methods:We determined the effects of cabazitaxel, a novel tubulin-binding taxane, and paclitaxel on paclitaxel-resistant, ABCB1-overexpressing KB-C2 and LLC-MDR1-WT cells and paclitaxel-resistant, ABCC10-overexpressing HEK293/ABCC10 cells by calculating the degree of drug resistance and measuring ATPase activity of the ABCB1 transporter. Results:Decreased resistance to cabazitaxel compared with paclitaxel was observed in KB-C2, LLC-MDR1-WT, and HEK293/ABCC10 cells. Moreover, cabazitaxel had low efficacy, whereas paclitaxel had high efficacy in stimulating the ATPase activity of ABCB1, indicating a direct interaction of both drugs with the transporter. Conclusion:ABCB1 and ABCC10 are not primary resistance factors for cabazitaxel compared with paclitaxel, suggesting that cabazitaxel may have a low affinity for these efflux transporters.

  15. The distribution of glutathione and homoglutathione in leaf, root and seed tissue of 73 species across the three sub-families of the Leguminosae.

    Science.gov (United States)

    Colville, Louise; Sáez, Clara M Blanco; Lewis, Gwilym P; Kranner, Ilse

    2015-07-01

    Homoglutathione (γ-glutamyl-cysteinyl-β-alanine) is a homologue of glutathione (γ-glutamyl-cysteinyl-glycine), which is a ubiquitous and indispensable tripeptide in eukaryotes with multi-facetted functions, many of which relate to cellular redox regulation. Homoglutathione is unique to the Leguminosae family, but studies of its occurrence have been restricted to the Papilionoideae subfamily, and almost exclusively to crop species. To determine whether the distribution of homoglutathione in the Leguminosae has a phylogenetic basis the occurrence of homoglutathione was investigated in the leaves, roots and seeds of 73 wild species of Leguminosae, representing 30 tribes across the Caesalpinioideae, Mimosoideae and Papilionoideae subfamilies. Homoglutathione was found only in the Papilionoideae, and was generally restricted to the 'Old World Clade'. It is proposed that homoglutathione may have arisen following a whole genome duplication event after the divergence of the Old World Clade. Homoglutathione is believed to fulfil the same functional roles as glutathione, but this study showed that homoglutathione and glutathione have different tissue-specific distribution patterns. Homoglutathione tended to occur more frequently in root tissue, and higher concentrations were found in leaves and roots, whereas glutathione tended to be present at the highest concentrations in seeds. This may reflect a distinct role for homoglutathione, particularly in roots, or an inability of homoglutathione to functionally replace glutathione in reproductive tissues. However, no relationships with environmental factors or nodulation were observed. Greater understanding of the factors that influence homoglutathione distribution may help to elucidate its unique function in some legume species.

  16. Odontomariinae, a new middle paleozoic subfamily of slit-bearing euophaloidean gastropods (Euophalomorpha, Gastropoda)

    Science.gov (United States)

    Fryda, J.; Heidelberger, D.; Blodgett, R.B.

    2006-01-01

    A new subfamily, the Odontomariinae subfam. nov., is established herein for a distinctive group of uncoiled, slit-bearing Middle Devonian euomphalid gastropods. Its taxonomic position is based on the recent discovery of open coiled protoconchs and it is placed within the Euomphalomorpha. The genera Odontomaria Odontomaria C. F. Roemer and Tubiconcha n. gen. belonging to this new subfamily are enlarged based on studies on new material of the following species: Odontomaria semiplicata (Sandberger & Sandberger), Odontomaria gracilis n. sp., Odontomaria jankei n. sp., Odontomaria cheeneetnukensis n. sp., Odontomaria cindiprellerae n. sp. and Tubiconcha leunissi (Heidelberger, 2001). Members of the Odontomariinae were mainly sedentary organisms in high-energy, moderately shallow water. ?? 2006 E. Schweizerbart'sche Verlagsbuchhandlung.

  17. The gymnosperm Pinus pinea contains both AOX gene subfamilies, AOX1 and AOX2.

    Science.gov (United States)

    Frederico, António Miguel; Zavattieri, Maria Amely; Campos, Maria Doroteia; Cardoso, Hélia Guerra; McDonald, Allison E; Arnholdt-Schmitt, Birgit

    2009-12-01

    The gymnosperm Pinus pinea L. (stone pine) is a typical Mediterranean pine used for nuts and timber production, and as an ornamental around the world. Pine genomes are large in comparison to other species. The hypothesis that retrotransposons, such as gymny, made a large contribution to this alteration in genome size was recently confirmed. However, P. pinea is unique in other various aspects. P. pinea demonstrates a different pattern of gymny organization than other Pinus subgenera. Additionally, P. pinea has a highly recalcitrant behaviour in relation to standard conifer protocols for the induction of somatic embryogenesis or rooting. Because such types of cell reprogramming can be explained as a reaction of plant cells to external stress, it is of special interest to study sequence peculiarities in stress-inducible genes, such as the alternative oxidase (AOX). This is the first report containing molecular evidence for the existence of AOX in gymnosperms at the genetic level. P. pinea AOXs were isolated by a polymerase chain reaction (PCR) approach and three genes were identified. Two of the genes belong to the AOX1 subfamily and one belongs to the AOX2 subfamily. The existence of both AOX subfamilies in gymnosperms is reported here for the first time. This discovery supports the hypothesis that AOX1 and AOX2 subfamilies arose prior to the separation of gymnosperms and angiosperms, and indicates that the AOX2 is absent in monocots because of subsequent gene loss events. Polymorphic P. pinea AOX1 sequences from a selected genetic clone are presented indicating non-allelic, non-synonymous and synonymous translation products.

  18. Data supporting the nuclear phylogenomics of the palm subfamily Arecoideae (Arecaceae).

    Science.gov (United States)

    Comer, Jason R; Zomlefer, Wendy B; Barrett, Craig F; Stevenson, Dennis Wm; Heyduk, Karolina; Leebens-Mack, James H

    2016-06-01

    This data article provides data and supplemental materials referenced in "Nuclear phylogenomics of the palm subfamily Arecoideae (Arecaceae)" (Comer et al., 2016) [1]. Raw sequence reads generated for this study are available through the Sequence Read Archive (SRA Study Accession: SRP061467). An aligned supermatrix of 168 nuclear genes for 35 taxa (34 palms and one outgroup taxon) is provided. Also provided are individual maximum likelihood gene trees used for the coalescent based analyses, output from the maximum parsimony analyses, and two figures.

  19. Salt-dependent regulation of a CNG channel subfamily in Arabidopsis

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    Wolff Patricia

    2009-11-01

    Full Text Available Abstract Background In Arabidopsis thaliana, the family of cyclic nucleotide-gated channels (CNGCs is composed of 20 members. Previous studies indicate that plant CNGCs are involved in the control of growth processes and responses to abiotic and biotic stresses. According to their proposed function as cation entry pathways these channels contribute to cellular cation homeostasis, including calcium and sodium, as well as to stress-related signal transduction. Here, we studied the expression patterns and regulation of CNGC19 and CNGC20, which constitute one of the five CNGC subfamilies. Results GUS, GFP and luciferase reporter assays were used to study the expression of CNGC19 and CNGC20 genes from Arabidopsis thaliana in response to developmental cues and salt stress. CNGC19 and CNGC20 were differentially expressed in roots and shoots. The CNGC19 gene was predominantly active in roots already at early growth stages. Major expression was observed in the phloem. CNGC20 showed highest promoter activity in mesophyll cells surrounding the veins. Its expression increased during development and was maximal in mature and senescent leaves. Both genes were upregulated in the shoot in response to elevated NaCl but not mannitol concentrations. While in the root, CNGC19 did not respond to changes in the salt concentration, in the shoot it was strongly upregulated in the observed time frame (6-72 hours. Salt-induction of CNGC20 was also observed in the shoot, starting already one hour after stress treatment. It occurred with similar kinetics, irrespective of whether NaCl was applied to roots of intact plants or to the petiole of detached leaves. No differences in K and Na contents of the shoots were measured in homozygous T-DNA insertion lines for CNGC19 and CNGC20, respectively, which developed a growth phenotype in the presence of up to 75 mM NaCl similar to that of the wild type. Conclusion Together, the results strongly suggest that both channels are

  20. Designing exons for human olfactory receptor gene subfamilies using a mathematical paradigm

    Indian Academy of Sciences (India)

    Sk Sarif Hassan; Pabitra Pal Choudhury; Amita Pal; R L Brahmachary; Arunava Goswami

    2010-09-01

    Ligands for only two human olfactory receptors are known. One of them, OR1D2, binds to Bourgeonal, a volatile chemical constituent of the fragrance of the mythical flower, Lily of the valley or Our Lady’s tears, Convallaria majalis (also the national flower of Finland). OR1D2, OR1D4 and OR1D5 are three full-length olfactory receptors present in an olfactory locus in the human genome. These receptors are more than 80% identical in DNA sequences and have 108 base pair mismatches among them. Apparently, these mismatch positions show no striking pattern using computer pattern recognition tools. In an attempt to find a mathematical rule in those mismatches, we find that an L-system generated sequence can be inserted into the OR1D2 subfamily-specific star model and novel full-length olfactory receptors can be generated. This remarkable mathematical principle could be utilized for making new subfamily olfactory receptor members from any olfactory receptor subfamily. The aroma and electronic nose industry might utilize this rule in future.

  1. Clonal Expansion and Cytotoxicity of TCRVβ Subfamily T Cells Induced by CML and K562 Cells

    Institute of Scientific and Technical Information of China (English)

    YupingZHang; YangqiuLi; ShaohuaChen; LijianYang; GengxinLuo; XueliZhang

    2004-01-01

    OBJECTIVE To investigate the anti-leukemia effect, the distribution and clonal expansion of TCRVβ subfamily T cells in T cells from cord blood and adult peripheral blood induced by CML cells and K562 cells in vitro. METHODS Peripheral blood T cells from one adult donor and 3 cases of cord blood were stimulated with CML cells and K562 cells and further amplified by a suspended T cell-bulk culture,in order to induce CML specific cytotoxic T lymphocytes. The induced T cells were further analyzed for the specific cytotoxicity in CML by LDH assay, the phenotype identification by indirect immunofiuorescence technique and the distribution and clonal expansion of TCRVβ subfamily by using reverse transcriptase-polymerase chain reaction (RT-PCR) and genescan analysis, respectively. RESULTS Oligoclonal and oligoclonal tendency T cells with higher specific cytotoxicity from cord blood and adult peripheral blood could be induced by stimulation with CML cells and K562 cells. CONCLUSIONS Specific cytotoxic T cells for an anti-CML effect could be induced by CML cells and K562 cells .The induced T cells which have the characteristic of specific cytotoxicity against CML cells may come from the clonal expansion of TCRVβ subfamily T cells.

  2. Computational identification and evolutional analysis of Piwi subfamily in 11 Drosophila species

    Institute of Scientific and Technical Information of China (English)

    Xue Zhou; Ya-Long Xu; Luo-Gen Cheng; Fei Li

    2008-01-01

    The complete genome sequences of 11 Drosophila species provide an opportu-nity to investigate the gene family evolution in closely related species.Drosophila Piwi subfamily,including three mcmbers,piwi,Aub and Ago3,has attracted increasing attention as it participates in the biogenesis of piRNA.Here,we identified 33 Piwi homologs from the genome of 11 Drosophila species.The full-length cDNA sequences of piwi and Aub genes were obtained by using New GENSCAN Web Server.The Ago3 homologs were diffcult regarding full-length information because they had long introns.The genomic structure of Piwf subfamily genes are highly conserved among diverse Drosophila species.Insect piwi and Aub genes have long first introns.The average length of the first intmn is 1 284 bp for piwf and 840 bp for Aub,Which is much larger than those of other introns(93 bp for Piwf and 54 bp for Aub).However,this phenomenon is not observed in mammalian piwi genes.We alSO found that there were abundant repeat sequences in both exons and introns of insect Ago3 genes.DHe to recent insertions of long terminal repeat elements in four Drosophila species.part of the third introns exhibit higher conservation thall adjacent exons and other introns.An evolutional tree created by Minimum Evolution method indicates that mamma-lian piwf genes are more closely related to the insect Ag03 Piwi subfamily.

  3. The DDX3 subfamily of the DEAD box helicases: divergent roles as unveiled by studying different organisms and in vitro assays.

    Science.gov (United States)

    Rosner, A; Rinkevich, B

    2007-01-01

    DDX3 (or Ded1p), the highly conserved subfamily of the DEAD-box RNA helicase family (40 members in humans), plays important roles in RNA metabolism. DDX3X and DDX3Y, the two human paralogous genes of this subfamily of proteins, have orthologous candidates in a diverse range of eukaryotes, from yeast and plants to animals. While DDX3Y, which is essential for normal spermatogenesis, is translated only in the testes, DDX3X protein is ubiquitously expressed, involved in RNA transcription, RNA splicing, mRNA transport, translation initiation and cell cycle regulation. Studies of recent years have revealed that DDX3X participates in HIV and hepatitis C viral infections, and in hepatocellular carcinoma, a complication of hepatitis B and hepatitis C infections. In the urochordates (i.e., Botryllus schlosseri) and in diverse invertebrate phyla (represented by model organisms such as: Drosophila, Hydra, Planaria), DDX3 proteins (termed also PL10) are involved in developmental pathways, highly expressed in adult undifferentiated soma and germ cells and in some adult and embryo's differentiating tissues. As the mechanistic and functional knowledge of DDX3 proteins is limited, we suggest assembling the available data on DDX3 proteins, from all studied organisms and in vitro assays, depicting a unified mechanistic scheme for DDX3 proteins' functions. Understanding the diverse functions of DDX3 in multicellular organisms may be particularly important for effective strategies of drug design.

  4. The subfamily-specific interaction between Kv2.1 and Kv6.4 subunits is determined by interactions between the N- and C-termini.

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    Elke Bocksteins

    Full Text Available The "silent" voltage-gated potassium (KvS channel subunit Kv6.4 does not form electrically functional homotetramers at the plasma membrane but assembles with Kv2.1 subunits, generating functional Kv2.1/Kv6.4 heterotetramers. The N-terminal T1 domain determines the subfamily-specific assembly of Kv1-4 subunits by preventing interactions between subunits that belong to different subfamilies. For Kv6.4, yeast-two-hybrid experiments showed an interaction of the Kv6.4 N-terminus with the Kv2.1 N-terminus, but unexpectedly also with the Kv3.1 N-terminus. We confirmed this interaction by Fluorescence Resonance Energy Transfer (FRET and co-immunoprecipitation (co-IP using N-terminal Kv3.1 and Kv6.4 fragments. However, full-length Kv3.1 and Kv6.4 subunits do not form heterotetramers at the plasma membrane. Therefore, additional interactions between the Kv6.4 and Kv2.1 subunits should be important in the Kv2.1/Kv6.4 subfamily-specificity. Using FRET and co-IP approaches with N- and C-terminal fragments we observed that the Kv6.4 C-terminus physically interacts with the Kv2.1 N-terminus but not with the Kv3.1 N-terminus. The N-terminal amino acid sequence CDD which is conserved between Kv2 and KvS subunits appeared to be a key determinant since charge reversals with arginine substitutions abolished the interaction between the N-terminus of Kv2.1 and the C-terminus of both Kv2.1 and Kv6.4. In addition, the Kv6.4(CKv3.1 chimera in which the C-terminus of Kv6.4 was replaced by the corresponding domain of Kv3.1, disrupted the assembly with Kv2.1. These results indicate that the subfamily-specific Kv2.1/Kv6.4 heterotetramerization is determined by interactions between Kv2.1 and Kv6.4 that involve both the N- and C-termini in which the conserved N-terminal CDD sequence plays a key role.

  5. Significant Microsynteny with New Evolutionary Highlights Is Detected through Comparative Genomic Sequence Analysis of Maize CCCH IX Gene Subfamily

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    Wei-Jun Chen

    2015-01-01

    Full Text Available CCCH zinc finger proteins, which are characterized by the presence of three cysteine residues and one histidine residue, play important roles in RNA processing in plants. Subfamily IX CCCH proteins were recently shown to function in stress tolerances. In this study, we analyzed CCCH IX genes in Zea mays, Oryza sativa, and Sorghum bicolor. These genes, which are almost intronless, were divided into four groups based on phylogenetic analysis. Microsynteny analysis revealed microsynteny in regions of some gene pairs, indicating that segmental duplication has played an important role in the expansion of this gene family. In addition, we calculated the dates of duplication by Ks analysis, finding that all microsynteny blocks were formed after the monocot-eudicot divergence. We found that deletions, multiplications, and inversions were shown to have occurred over the course of evolution. Moreover, the Ka/Ks ratios indicated that the genes in these three grass species are under strong purifying selection. Finally, we investigated the evolutionary patterns of some gene pairs conferring tolerance to abiotic stress, laying the foundation for future functional studies of these transcription factors.

  6. Phylogeny and evolutionary patterns in the Dwarf crayfish subfamily (Decapoda: Cambarellinae.

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    Carlos Pedraza-Lara

    Full Text Available The Dwarf crayfish or Cambarellinae, is a morphologically singular subfamily of decapod crustaceans that contains only one genus, Cambarellus. Its intriguing distribution, along the river basins of the Gulf Coast of United States (Gulf Group and into Central México (Mexican Group, has until now lacked of satisfactory explanation. This study provides a comprehensive sampling of most of the extant species of Cambarellus and sheds light on its evolutionary history, systematics and biogeography. We tested the impact of Gulf Group versus Mexican Group geography on rates of cladogenesis using a maximum likelihood framework, testing different models of birth/extinction of lineages. We propose a comprehensive phylogenetic hypothesis for the subfamily based on mitochondrial and nuclear loci (3,833 bp using Bayesian and Maximum Likelihood methods. The phylogenetic structure found two phylogenetic groups associated to the two main geographic components (Gulf Group and Mexican Group and is partially consistent with the historical structure of river basins. The previous hypothesis, which divided the genus into three subgenera based on genitalia morphology was only partially supported (P = 0.047, resulting in a paraphyletic subgenus Pandicambarus. We found at least two cases in which phylogenetic structure failed to recover monophyly of recognized species while detecting several cases of cryptic diversity, corresponding to lineages not assigned to any described species. Cladogenetic patterns in the entire subfamily are better explained by an allopatric model of speciation. Diversification analyses showed similar cladogenesis patterns between both groups and did not significantly differ from the constant rate models. While cladogenesis in the Gulf Group is coincident in time with changes in the sea levels, in the Mexican Group, cladogenesis is congruent with the formation of the Trans-Mexican Volcanic Belt. Our results show how similar allopatric

  7. The formation of the polyploid hybrids from different subfamily fish crossings and its evolutionary significance.

    Science.gov (United States)

    Liu, Shaojun; Qin, Qinbo; Xiao, Jun; Lu, Wenting; Shen, Jiamin; Li, Wei; Liu, Jifang; Duan, Wei; Zhang, Chun; Tao, Min; Zhao, Rurong; Yan, Jinpeng; Liu, Yun

    2007-06-01

    This study provides genetic evidences at the chromosome, DNA content, DNA fragment and sequence, and morphological levels to support the successful establishment of the polyploid hybrids of red crucian carp x blunt snout bream, which belonged to a different subfamily of fish (Cyprininae subfamily and Cultrinae subfamily) in the catalog. We successfully obtained the sterile triploid hybrids and bisexual fertile tetraploid hybrids of red crucian carp (RCC) (female symbol) x blunt snout bream (BSB) (male symbol) as well as their pentaploid hybrids. The triploid hybrids possessed 124 chromosomes with two sets from RCC and one set from BSB; the tetraploid hybrids had 148 chromosomes with two sets from RCC and two sets from BSB. The females of tetraploid hybrids produced unreduced tetraploid eggs that were fertilized with the haploid sperm of BSB to generate pentaploid hybrids with 172 chromosomes with three sets from BSB and two sets from RCC. The ploidy levels of triploid, tetraploid, and pentaploid hybrids were confirmed by counting chromosomal number, forming chromosomal karyotype, and measuring DNA content and erythrocyte nuclear volume. The similar and different DNA fragments were PCR amplified and sequenced in triploid, tetraploid hybrids, and their parents, indicating their molecular genetic relationship and genetic markers. In addition, this study also presents results about the phenotypes and feeding habits of polyploid hybrids and discusses the formation mechanism of the polyploid hybrids. It is the first report on the formation of the triploid, tetraploid, and pentaploid hybrids by crossing parents with a different chromosome number in vertebrates. The formation of the polyploid hybrids is potentially interesting in both evolution and fish genetic breeding.

  8. Identification and characterization of a novel gene differentially expressed in zebrafish cross-subfamily cloned embryos

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    Wang Ya-Ping

    2008-03-01

    Full Text Available Abstract Background Cross-species nuclear transfer has been shown to be a potent approach to retain the genetic viability of a certain species near extinction. However, most embryos produced by cross-species nuclear transfer were compromised because that they were unable to develop to later stages. Gene expression analysis of cross-species cloned embryos will yield new insights into the regulatory mechanisms involved in cross-species nuclear transfer and embryonic development. Results A novel gene, K31, was identified as an up-regulated gene in fish cross-subfamily cloned embryos using SSH approach and RACE method. K31 complete cDNA sequence is 1106 base pairs (bp in length, with a 342 bp open reading frame (ORF encoding a putative protein of 113 amino acids (aa. Comparative analysis revealed no homologous known gene in zebrafish and other species database. K31 protein contains a putative transmembrane helix and five putative phosphorylation sites but without a signal peptide. Expression pattern analysis by real time RT-PCR and whole-mount in situ hybridization (WISH shows that it has the characteristics of constitutively expressed gene. Sub-cellular localization assay shows that K31 protein can not penetrate the nuclei. Interestingly, over-expression of K31 gene can cause lethality in the epithelioma papulosum cyprinid (EPC cells in cell culture, which gave hint to the inefficient reprogramming events occurred in cloned embryos. Conclusion Taken together, our findings indicated that K31 gene is a novel gene differentially expressed in fish cross-subfamily cloned embryos and over-expression of K31 gene can cause lethality of cultured fish cells. To our knowledge, this is the first report on the determination of novel genes involved in nucleo-cytoplasmic interaction of fish cross-subfamily cloned embryos.

  9. Reassessment of Species Diversity of the Subfamily Denticollinae (Coleoptera: Elateridae through DNA Barcoding.

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    Taeman Han

    Full Text Available The subfamily Denticollinae is a taxonomically diverse group in the family Elateridae. Denticollinae includes many morphologically similar species and crop pests, as well as many undescribed species at each local fauna. To construct a rapid and reliable identification system for this subfamily, the effectiveness of molecular species identification was assessed based on 421 cytochrome c oxidase subunit I (COI sequences of 84 morphologically identified species. Among the 84 morphospecies, molecular species identification of 60 species (71.4% was consistent with their morphological identifications. Six cryptic and/or pseudocryptic species with large genetic divergence (>5% were confirmed by their sympatric or allopatric distributions. However, 18 species, including a subspecies, had ambiguous genetic distances and shared overlapping intra- and interspecific genetic distances (range: 2.12%-3.67% suggesting incomplete lineage sorting, introgression of mitochondrial genome, or affection by endosymbionts, such as Wolbachia infection, between species and simple genetic variation within species. In this study, we propose a conservative threshold of 3.6% for convenient molecular operational taxonomic unit (MOTU identification in the subfamily Denticollinae based on the results of pairwise genetic distances analyses using neighbor-joining, mothur, Automatic Barcode Gap Discovery analysis, and tree-based species delimitation by Poisson Tree Processes analysis. Using the 3.6% threshold, we identified 87 MOTUs and found 8 MOTUs in the interval between 2.5% to 3.5%. Evaluation of MOTUs identified in this range requires integrative species delimitation, including review of morphological and ecological differences as well as sensitive genetic markers. From this study, we confirmed that COI sequence is useful for reassessing species diversity for polymorphic and polytypic species occurring in sympatric and allopatric distributions, and for a single species having

  10. The SIDER2 elements, interspersed repeated sequences that populate the Leishmania genomes, constitute subfamilies showing chromosomal proximity relationship

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    Thomas M Carmen

    2008-06-01

    Full Text Available Abstract Background Protozoan parasites of the genus Leishmania are causative agents of a diverse spectrum of human diseases collectively known as leishmaniasis. These eukaryotic pathogens that diverged early from the main eukaryotic lineage possess a number of unusual genomic, molecular and biochemical features. The completion of the genome projects for three Leishmania species has generated invaluable information enabling a direct analysis of genome structure and organization. Results By using DNA macroarrays, made with Leishmania infantum genomic clones and hybridized with total DNA from the parasite, we identified a clone containing a repeated sequence. An analysis of the recently completed genome sequence of L. infantum, using this repeated sequence as bait, led to the identification of a new class of repeated elements that are interspersed along the different L. infantum chromosomes. These elements turned out to be homologues of SIDER2 sequences, which were recently identified in the Leishmania major genome; thus, we adopted this nomenclature for the Leishmania elements described herein. Since SIDER2 elements are very heterogeneous in sequence, their precise identification is rather laborious. We have characterized 54 LiSIDER2 elements in chromosome 32 and 27 ones in chromosome 20. The mean size for these elements is 550 bp and their sequence is G+C rich (mean value of 66.5%. On the basis of sequence similarity, these elements can be grouped in subfamilies that show a remarkable relationship of proximity, i.e. SIDER2s of a given subfamily locate close in a chromosomal region without intercalating elements. For comparative purposes, we have identified the SIDER2 elements existing in L. major and Leishmania braziliensis chromosomes 32. While SIDER2 elements are highly conserved both in number and location between L. infantum and L. major, no such conservation exists when comparing with SIDER2s in L. braziliensis chromosome 32. Conclusion

  11. Phthiria sharafi sp. nov., a new record of the subfamily Phthiriinae (Bombyliidae, Diptera) from Saudi Arabia.

    Science.gov (United States)

    El-Hawagry, Magdi S; Al Dhafer, Hathal M

    2014-10-10

    This new species (Phthiria sharafi sp. nov.) represents the first record of the subfamily Phthiriinae (Bombyliidae, Diptera) from Saudi Arabia. The species was collected from Garf Raydah Protected Area, Abha, Asir Province, south-western part of Saudi Arabia, using a Malaise trap erected in a site rich in olive, cactus and Juniper trees. The type locality has an Afrotropical influence, with the Afrotropical elements predominant, and a closer affiliation to the Afrotropical region than to the Palearctic region or the Eremic zone. 

  12. Data supporting the nuclear phylogenomics of the palm subfamily Arecoideae (Arecaceae

    Directory of Open Access Journals (Sweden)

    Jason R. Comer

    2016-06-01

    Full Text Available This data article provides data and supplemental materials referenced in “Nuclear phylogenomics of the palm subfamily Arecoideae (Arecaceae” (Comer et al., 2016 [1]. Raw sequence reads generated for this study are available through the Sequence Read Archive (SRA Study Accession: SRP061467. An aligned supermatrix of 168 nuclear genes for 35 taxa (34 palms and one outgroup taxon is provided. Also provided are individual maximum likelihood gene trees used for the coalescent based analyses, output from the maximum parsimony analyses, and two figures.

  13. An annotated catalogue of the subfamily Orthotylinae (Hemiptera: Heteroptera: Miridae from the Korean Peninsula

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    Sunghoon Jung

    2017-09-01

    Full Text Available This paper provides an annotated catalogue of the plant bugs, subfamily Orthotylinae (Heteroptera: Miridae from the Korean Peninsula. In this study, a total of 41 species are enumerated, including four new records from the Korean Peninsula: Heterocordylus alutaceus Kulik 1965, Malacocorisella endoi Yasunaga, 1999, Orthotylus interpositus Schmidt, 1938, and Strongylocoris leucocephalus (Linnaeus, 1758. Distribution data and bibliographical references of each taxon are included. Biological notes (e.g. host and/or habitat based on the local specimens of the Korean Peninsula are also presented.

  14. Linear array of conserved sequence motifs to discriminate protein subfamilies: study on pyridine nucleotide-disulfide reductases

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    De Las Rivas Javier

    2007-03-01

    Full Text Available Abstract Background The pyridine nucleotide disulfide reductase (PNDR is a large and heterogeneous protein family divided into two classes (I and II, which reflect the divergent evolution of its characteristic disulfide redox active site. However, not all the PNDR members fit into these categories and this suggests the need of further studies to achieve a more comprehensive classification of this complex family. Results A workflow to improve the clusterization of protein families based on the array of linear conserved motifs is designed. The method is applied to the PNDR large family finding two main groups, which correspond to PNDR classes I and II. However, two other separate protein clusters, previously classified as class I in most databases, are outgrouped: the peroxide reductases (NAOX, NAPE and the type II NADH dehydrogenases (NDH-2. In this way, two novel PNDR classes III and IV for NAOX/NAPE and NDH-2 respectively are proposed. By knowledge-driven biochemical and functional data analyses done on the new class IV, a linear array of motifs putatively related to Cu(II-reductase activity is detected in a specific subset of NDH-2. Conclusion The results presented are a novel contribution to the classification of the complex and large PNDR protein family, supporting its reclusterization into four classes. The linear array of motifs detected within the class IV PNDR subfamily could be useful as a signature for a particular subgroup of NDH-2.

  15. Paralog-divergent Features May Help Reduce Off-target Effects of Drugs: Hints from Glucagon Subfamily Analysis

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    Zhining Sa

    2017-08-01

    Full Text Available Side effects from targeted drugs remain a serious concern. One reason is the nonselective binding of a drug to unintended proteins such as its paralogs, which are highly homologous in sequences and have similar structures and drug-binding pockets. To identify targetable differences between paralogs, we analyzed two types (type-I and type-II of functional divergence between two paralogs in the known target protein receptor family G-protein coupled receptors (GPCRs at the amino acid level. Paralogous protein receptors in glucagon-like subfamily, glucagon receptor (GCGR and glucagon-like peptide-1 receptor (GLP-1R, exhibit divergence in ligands and are clinically validated drug targets for type 2 diabetes. Our data showed that type-II amino acids were significantly enriched in the binding sites of antagonist MK-0893 to GCGR, which had a radical shift in physicochemical properties between GCGR and GLP-1R. We also examined the role of type-I amino acids between GCGR and GLP-1R. The divergent features between GCGR and GLP-1R paralogs may be helpful in their discrimination, thus enabling the identification of binding sites to reduce undesirable side effects and increase the target specificity of drugs.

  16. Paralog-divergent Features May Help Reduce Off-target Effects of Drugs: Hints from Glucagon Subfamily Analysis.

    Science.gov (United States)

    Sa, Zhining; Zhou, Jingqi; Zou, Yangyun; Su, Zhixi; Gu, Xun

    2017-08-01

    Side effects from targeted drugs remain a serious concern. One reason is the nonselective binding of a drug to unintended proteins such as its paralogs, which are highly homologous in sequences and have similar structures and drug-binding pockets. To identify targetable differences between paralogs, we analyzed two types (type-I and type-II) of functional divergence between two paralogs in the known target protein receptor family G-protein coupled receptors (GPCRs) at the amino acid level. Paralogous protein receptors in glucagon-like subfamily, glucagon receptor (GCGR) and glucagon-like peptide-1 receptor (GLP-1R), exhibit divergence in ligands and are clinically validated drug targets for type 2 diabetes. Our data showed that type-II amino acids were significantly enriched in the binding sites of antagonist MK-0893 to GCGR, which had a radical shift in physicochemical properties between GCGR and GLP-1R. We also examined the role of type-I amino acids between GCGR and GLP-1R. The divergent features between GCGR and GLP-1R paralogs may be helpful in their discrimination, thus enabling the identification of binding sites to reduce undesirable side effects and increase the target specificity of drugs. Copyright © 2017 The Authors. Production and hosting by Elsevier B.V. All rights reserved.

  17. SLIDE, the Protein Interacting Domain of Imitation Switch Remodelers, Binds DDT-Domain Proteins of Different Subfamilies in Chromatin Remodeling Complexes

    Institute of Scientific and Technical Information of China (English)

    Jiaqiang Dong; Zheng Gao; Shujing Liu; Guang Li; Zhongnan Yang; Hai Huang; Lin Xu

    2013-01-01

    The Imitation Switch (ISWI) type adenosine triphosphate (ATP)-dependent chromatin remodeling factors are conserved proteins in eukaryotes, and some of them are known to form stable remodeling complexes with members from a family of proteins, termed DDT-domain proteins. Although it is well documented that ISWIs play important roles in different biological processes in many eukaryotic species, the molecular basis for protein interactions in ISWI complexes has not been fully addressed. Here, we report the identification of interaction domains for both ISWI and DDT-domain proteins. By analyzing CHROMATIN REMODELING11 (CHR11) and RINGLET1 (RLT1), an Arabidopsis thaliana ISWI (AtISWI) and AtDDT-domain protein, respectively, we show that the SLIDE domain of CHR11 and the DDT domain together with an adjacent sequence of RLT1 are responsible for their binding. The Arabidopsis genome contains at least 12 genes that encode DDT-domain proteins, which could be grouped into five subfamilies based on the sequence similarity. The SLIDE domain of AtISWI is able to bind members from different AtDDT subfamilies. Moreover, a human ISWI protein SNF2H is capable of binding AtDDT-domain proteins through its SLIDE domain, suggesting that binding to DDT-domain proteins is a conserved biochemical function for the SLIDE domain of ISWIs in eukaryotes.

  18. A consistent nomenclature of antimicrobial peptides isolated from frogs of the subfamily Phyllomedusinae.

    Science.gov (United States)

    Amiche, Mohamed; Ladram, Ali; Nicolas, Pierre

    2008-11-01

    A growing number of cationic antimicrobial peptides have been isolated from the skin of hylid frogs belonging to the Phyllomedusinae subfamily. The amino acid sequences of these peptides are currently located in several databases under identifiers with no consistent system of nomenclature to describe them. In order to provide a workable terminology for antimicrobial peptides from Phyllomedusid frogs, we have made a systematic effort to collect, analyze, and classify all the Phyllomedusid peptide sequences available in databases. We propose that frogs belonging to the Phyllomedusinae subfamily should be described by the species names set out in Amphibian Species of the World: http://research.amnh.org/herpetology/amphibia/index.php, American Museum of Natural History, New York, USA. Multiple alignments analysis of at least 80 antimicrobial peptides isolated from 12 Phyllomedusinae species were distributed in seven distinct peptide families including dermaseptin, phylloseptin, plasticin, dermatoxin, phylloxin, hyposin and orphan peptides, and will be considered as the name of the headgroup of each family. The parent peptide's name should be followed by the first upper letter of the species for orthologous peptides and publication date determines priority. For example, the abbreviation B for bicolor and H for hypochondrialis. When two species begin with the same letter, two letters in upper case should be used (the first letter followed by the second or the third letter and so on). For example, the abbreviation DI for distincta, DU for duellmani, VA for vaillanti and VN for vanzolinii. Paralogous peptides should bear letter(s) in upper case followed by numbers.

  19. Myosin Binding Protein-C Slow: An Intricate Subfamily of Proteins

    Directory of Open Access Journals (Sweden)

    Maegen A. Ackermann

    2010-01-01

    Full Text Available Myosin binding protein C (MyBP-C consists of a family of thick filament associated proteins. Three isoforms of MyBP-C exist in striated muscles: cardiac, slow skeletal, and fast skeletal. To date, most studies have focused on the cardiac form, due to its direct involvement in the development of hypertrophic cardiomyopathy. Here we focus on the slow skeletal form, discuss past and current literature, and present evidence to support that: (i MyBP-C slow comprises a subfamily of four proteins, resulting from complex alternative shuffling of the single MyBP-C slow gene, (ii the four MyBP-C slow isoforms are expressed in variable amounts in different skeletal muscles, (iii at least one MyBP-C slow isoform is preferentially found at the periphery of M-bands and (iv the MyBP-C slow subfamily may play important roles in the assembly and stabilization of sarcomeric M- and A-bands and regulate the contractile properties of the actomyosin filaments.

  20. Characteristics of the LrhA subfamily of transcriptional regulators from Sinorhizobium meliloti

    Institute of Scientific and Technical Information of China (English)

    Mingsheng Qi; Li Luo; Haiping Cheng; Jiabi Zhu; Guanqiao Yu

    2008-01-01

    In our previous work, we identified 94 putative genes encoding LysR-type transcriptional regulators from Sinorhizobium meliloti. All of these putative lysR genes were mutagenized using plasmid insertions to determine their phenotypes. Six LysR-type regulators, encoded by mutants SMa1979, SMb20715, SMc00820, SMc04163, SMc03975,and SMc04315, showed similar amino acid sequences (30%)and shared the conserved DNA-binding domain with LrhA,HexA, or DgdR. Phenotype analysis of these gene mutants indicated that the regulators control the swimming behaviors of the bacteria, production of quorum-sensing signals, and secretion of extracellular proteins. These characteristics are very similar to those of LrhA, HexA, and DgdR.Thus, we refer to this group as the LrhA subfamily. Sequence analysis showed that a great number of homologous genes of the LrhA subfamily were distributed in the α,β, and γsubdivisions of proteobacteria, and a few in actinobacteria. These findings could provide new clues to the roles of the LysR gene family.

  1. Flight patterns and sex ratio of beetles of the subfamily Dynastinae (Coleoptera, Melolonthidae

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    Larissa Simões Corrêa de Albuquerque

    2016-09-01

    Full Text Available ABSTRACT Dynastinae is one of the most representative subfamilies of Melolonthidae (Scarabaeoidea and has considerable ecological importance due mainly to interactions with plants of the families Araceae and Annonaceae. This relationship has led to the evolution of nocturnal activity patterns, which are influenced by environmental conditions. In the present study, abiotic factors were investigated to comprehend the influence on the flight patterns and identify the sex ratio of beetles from this subfamily. A study was conducted at Campo de Instrução Marechal Newton Cavalcanti in northeastern Brazil between December 2010 and November 2011. Thirteen species of Dynastinae were identified, most of which were from the genus Cyclocephala. Abundance and richness were greater in the dry season. Six species exhibited peak flight activity at specific periods of the night. More females than males were recorded for Cyclocephala distincta and C. paraguayensis. The present findings suggest that rainfall reduces the flight activity of these beetles and different time schedules may be related to mating behavior, foraging behavior and the avoidance of interspecific resource competition.

  2. Two CRM protein subfamilies cooperate in the splicing of group IIB introns in chloroplasts.

    Science.gov (United States)

    Asakura, Yukari; Bayraktar, Omer Ali; Barkan, Alice

    2008-11-01

    Chloroplast genomes in angiosperms encode approximately 20 group II introns, approximately half of which are classified as subgroup IIB. The splicing of all but one of the subgroup IIB introns requires a heterodimer containing the peptidyl-tRNA hydrolase homolog CRS2 and one of two closely related proteins, CAF1 or CAF2, that harbor a recently recognized RNA binding domain called the CRM domain. Two CRS2/CAF-dependent introns require, in addition, a CRM domain protein called CFM2 that is only distantly related to CAF1 and CAF2. Here, we show that CFM3, a close relative of CFM2, associates in vivo with those CRS2/CAF-dependent introns that are not CFM2 ligands. Mutant phenotypes in rice and Arabidopsis support a role for CFM3 in the splicing of most of the introns with which it associates. These results show that either CAF1 or CAF2 and either CFM2 or CFM3 simultaneously bind most chloroplast subgroup IIB introns in vivo, and that the CAF and CFM subunits play nonredundant roles in splicing. These results suggest that the expansion of the CRM protein family in plants resulted in two subfamilies that play different roles in group II intron splicing, with further diversification within a subfamily to accommodate multiple intron ligands.

  3. Phylogenetic relationships between flies of the Tephritinae subfamily (Diptera, Tephritidae) and their symbiotic bacteria.

    Science.gov (United States)

    Mazzon, Luca; Martinez-Sañudo, Isabel; Simonato, Mauro; Squartini, Andrea; Savio, Claudia; Girolami, Vincenzo

    2010-07-01

    The Tephritinae is considered the most specialized subfamily of fruit flies, predominantly infesting flowerheads of Asteraceae. Some species are known to host specific non-culturable symbiont bacteria ("Candidatus Stammerula spp.") in the midgut. In this work we (i) examined the phylogenetic relationships among the insect hosts, (ii) investigated the presence of bacteria in other hitherto unexamined species, and (iii) evaluated the phylogenetic congruence between insects and symbionts. A total of 33 Tephritinae species in 17 different genera were analyzed. Two regions of the mitochondrial DNA (16S rDNA and COI-tRNALeu-COII) were examined in the insect host, while the 16S was analyzed in the bacteria. From the phylogenetic trees, four of the five tribes considered were statistically supported by each of the clustering methods used. Species belonging to the tribe Noeetini never clustered at significant levels. The phylogenetic COI-tRNALeu-COII tree showed internal nodes more highly supported than the 16S phylogeny. The analysis of the distribution of symbiosis across the subfamily has highlighted the presence of bacteria only in the tribe Tephritini and in the genus Noeeta from the tribe Noeetini. A cophylogenetic analysis revealed a substantial congruence between hosts and symbionts. The interesting exceptions can be justified by events like losses, duplications and hosts switching opportunities, which are likely to arise during the biological cycle of the fly in consideration of the extracellular status of these symbionts.

  4. A new genus of the subfamily Cillaeinae (Coleoptera, Nitidulidae) from the Philippines and New Guinea with notes on the taxonomy and phylogeny of the subfamily.

    Science.gov (United States)

    Kirejtshuk, Alexander G; Kovalev, Alexey V

    2016-12-06

    Allenipeplus gen. nov. represented by A. philippinensis sp. nov., type species (Philippines, Luzon), A. alius sp. nov. (Philippines, Mindoro), A. harmonicus sp. nov. (Philippines, Mindanao) and A. vitellinus sp. nov. (Indonesian New Guinea), is described. This new genus combines characters with a mosaic spread among other cillaeine genera. We present a wide comparison of genera among the subfamily Cillaeinae, making it possible to elaborate a detailed diagnosis of the new genus and trace some order in character patterns and propose a hypothesis on the relationship of this genus to other groups known from the Indo-Malayan and Australian Regions. A detailed diagnosis of the new genus and key to the new species are given. The Adocimus-complex of the related genera including Allenipeplus gen. nov., Adocimus Murray, 1864, Ithyphenes Murray, 1864, Platynema Ritsema, 1885 and probably Brittonema Kirejtshuk, 2011 is defined. Some notes on the taxonomy of the genera Liparopeplus Murray, 1864 and Xanthopeplus Fairmaire, 1880, stat. nov. are given. Additionally, designation of a lectotype for Liparopeplus colastoides Murray, 1864 is made.

  5. The Evolutionary History of R2R3-MYB Proteins Across 50 Eukaryotes: New Insights Into Subfamily Classification and Expansion.

    Science.gov (United States)

    Du, Hai; Liang, Zhe; Zhao, Sen; Nan, Ming-Ge; Tran, Lam-Son Phan; Lu, Kun; Huang, Yu-Bi; Li, Jia-Na

    2015-06-05

    R2R3-MYB proteins (2R-MYBs) are one of the main transcription factor families in higher plants. Since the evolutionary history of this gene family across the eukaryotic kingdom remains unknown, we performed a comparative analysis of 2R-MYBs from 50 major eukaryotic lineages, with particular emphasis on land plants. A total of 1548 candidates were identified among diverse taxonomic groups, which allowed for an updated classification of 73 highly conserved subfamilies, including many newly identified subfamilies. Our results revealed that the protein architectures, intron patterns, and sequence characteristics were remarkably conserved in each subfamily. At least four subfamilies were derived from early land plants, 10 evolved from spermatophytes, and 19 from angiosperms, demonstrating the diversity and preferential expansion of this gene family in land plants. Moreover, we determined that their remarkable expansion was mainly attributed to whole genome and segmental duplication, where duplicates were preferentially retained within certain subfamilies that shared three homologous intron patterns (a, b, and c) even though up to 12 types of patterns existed. Through our integrated distributions, sequence characteristics, and phylogenetic tree analyses, we confirm that 2R-MYBs are old and postulate that 3R-MYBs may be evolutionarily derived from 2R-MYBs via intragenic domain duplication.

  6. Getting from A to B-exploring the activation motifs of the class B adhesion G protein-coupled receptor subfamily G member 4/GPR112

    DEFF Research Database (Denmark)

    Cornelia Peeters, Miriam; Mos, Iris; Lenselink, Eelke B;

    2016-01-01

    The adhesion G protein-coupled receptors (ADGRs/class B2 G protein-coupled receptors) constitute an ancient family of G protein-coupled receptors that have recently been demonstrated to play important roles in cellular and developmental processes. Here, we describe a first insight...... into the structure-function relationship of ADGRs using the family member ADGR subfamily G member 4 (ADGRG4)/GPR112 as a model receptor. In a bioinformatics approach, we compared conserved, functional elements of the well-characterized class A and class B1 secretin-like G protein-coupled receptors with the ADGRs. We...... identified several potential equivalent motifs and subjected those to mutational analysis. The importance of the mutated residues was evaluated by examining their effect on the high constitutive activity of the N-terminally truncated ADGRG4/GPR112 in a 1-receptor-1-G protein Saccharomyces cerevisiae...

  7. The role of morpho-anatomical traits of the leaves in the taxonomy of Kalanchoideae Berg. subfamily (Crassulaceae DC.

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    Myhajlo A. Chernetskyy

    2012-03-01

    Full Text Available The paper presents the results of the analysis of the morphological and anatomical structure of leaves of 35 species of the genus Kalanchoë Adans. (Crassulaceae DC. in the taxonomic aspect of the subfamily Kalanchoideae Berg. Based on own studies and literature analyses of the flower morphology, embryology, karyology, vascular anatomy of stem and molecular genetics, the author has found that the most appropriate taxonomic system of the subfamily Kalanchoideae assumes existence of one genus Kalanchoë divided into three sections:Bryophyllum (Salisb. Boit. & Mann.,Eukalanchoë Boit. & Mann. and Kitchingia (Bak. Boit. & Mann. Distinguishing three separate genera Bryophyllum Salisb., Kalanchoё Adans. and Kitchingia Bak., as has been the case throughout the history of the subfamily Kalanchoideae, is hardly possible due to existence of “intermediate” species.

  8. Identification and characterization of RBEL1 subfamily of GTPases in the Ras superfamily involved in cell growth regulation.

    Science.gov (United States)

    Montalbano, JoAnne; Lui, Ki; Sheikh, M Saeed; Huang, Ying

    2009-07-03

    Recently, we reported the identification of a novel gene named RBEL1 (Rab-like protein 1) and characterized its two encoded isoforms, RBEL1A and RBEL1B, that function as novel GTPases of Ras superfamily. Here we report the identification of two additional splice variants of RBEL1 that we have named RBEL1C and -D. All four RBEL1 isoforms (A, B, C, and D) have identical N termini harboring the Rab-like GTPase domains but contain variable C termini. Although all isoforms can be detected in both cytoplasm and nucleus, RBEL1A is predominantly cytoplasmic, whereas RBEL1B is mostly nuclear. RBEL1C and -D, by contrast, are evenly distributed between the cytoplasm and nucleus. Furthermore, all four RBEL1 proteins are also capable of associating with cellular membrane. The RBEL1 proteins also exhibit a unique nucleotide-binding potential and, whereas the larger A and B isoforms are mainly GTP-bound, the smaller C and D variants bind to both GTP and GDP. Furthermore, a regulatory region at amino acid position 236-302 immediately adjacent to the GTP-binding domain is important for GTP-binding potential of RBEL1A, because deletion of this region converts RBEL1A from predominantly GTP-bound to GDP-bound. RBEL1 knockdown via RNA interference results in marked cell growth suppression, which is associated with morphological and biochemical features of apoptosis as well as inhibition of extracellular signal-regulated kinase phosphorylation. Taken together, our results indicate that RBEL1 proteins are linked to cell growth and survival and possess unique biochemical, cellular, and functional characteristics and, therefore, appear to form a novel subfamily of GTPases within the Ras superfamily.

  9. The Atypical Response Regulator Protein ChxR Has Structural Characteristics and Dimer Interface Interactions That Are Unique within the OmpR/PhoB Subfamily

    Energy Technology Data Exchange (ETDEWEB)

    Hickey, John M.; Lovell, Scott; Battaile, Kevin P.; Hu, Lei; Middaugh, C. Russell; Hefty, P. Scott (Kansas); (HWMRI)

    2013-05-29

    Typically as a result of phosphorylation, OmpR/PhoB response regulators form homodimers through a receiver domain as an integral step in transcriptional activation. Phosphorylation stabilizes the ionic and hydrophobic interactions between monomers. Recent studies have shown that some response regulators retain functional activity in the absence of phosphorylation and are termed atypical response regulators. The two currently available receiver domain structures of atypical response regulators are very similar to their phospho-accepting homologs, and their propensity to form homodimers is generally retained. An atypical response regulator, ChxR, from Chlamydia trachomatis, was previously reported to form homodimers; however, the residues critical to this interaction have not been elucidated. We hypothesize that the intra- and intermolecular interactions involved in forming a transcriptionally competent ChxR are distinct from the canonical phosphorylation (activation) paradigm in the OmpR/PhoB response regulator subfamily. To test this hypothesis, structural and functional studies were performed on the receiver domain of ChxR. Two crystal structures of the receiver domain were solved with the recently developed method using triiodo compound I3C. These structures revealed many characteristics unique to OmpR/PhoB subfamily members: typical or atypical. Included was the absence of two {alpha}-helices present in all other OmpR/PhoB response regulators. Functional studies on various dimer interface residues demonstrated that ChxR forms relatively stable homodimers through hydrophobic interactions, and disruption of these can be accomplished with the introduction of a charged residue within the dimer interface. A gel shift study with monomeric ChxR supports that dimerization through the receiver domain is critical for interaction with DNA.

  10. Nasal mites of the subfamily Speleognathinae (Ereynetidae) from birds in Texas.

    Science.gov (United States)

    Pence, D B; Casto, S D

    1976-06-01

    Nasal mites of the subfamily Speleognathinae were recovered from several species of birds in Texas. New host records include Ophthalmophagus striatus (Crossley) 1952 from Columbigallina passerina, Boydaia clarki Fain 1963 from Callipepla squamata, Boydaia falconis Fain 1956 from Falco sparverius, and Boydaia tyrannus Ford 1959 from Myiarchus cinerascens. Also recovered was Astrida coccyzae Pence 1972 from Coccyzus americanus. Boydaia pheucticola sp. n. from Pheucticus melanocephalus is described. It differs from similar species in the adult female by having the coxal setae formula 2-1-2-0, sensillae clavate but not globose or subglobose, and interior seta on coxa I reduced in size but not vestigial. The larva is differentiated by the modified legs II with one long recurved hooklike claw and a shorter curved claw.

  11. Quill mites of the subfamily Picobiinae (Acari: Syringophilidae) associated with woodpeckers (Aves: Piciformes: Picidae).

    Science.gov (United States)

    Skoracki, Maciej; Unsoeld, Markus; Kavetska, Katarzyna; Kaszewska, Katarzyna

    2014-03-01

    The paper contains a review of quill mites of the subfamily Picobiinae (Acari: Prostigmata: Syringophilidae) associated with woodpeckers (Aves: Piciformes: Picidae). Three new species are described: Picobia mentalis Skoracki et Unsoeld sp. nov. from Picus mentalis Temminck, Neopicobia ea Skoracki et Unsoeld sp. nov. from Celeus flavus (St. Mueller) (type host), C. elegans (St. Mueller), C. torquatus (Boddaert), and Neopicobia freya Skoracki et Unsoeld sp. nov. from Dryocopus galeatus (Temminck) (type host) and Piculus rubiginosus (Swainson). Additionally, six new host species for Picobia heeri Haller, 1878 and 12 new host species for Picobia dryobatis (Fritsch, 1956) are reported. A complete list of the picobiines parasitising birds of the family Picidae is presented in the tabular form.

  12. Molecular phylogeny of moth-specialized spider sub-family Cyrtarachninae, which includes bolas spiders.

    Science.gov (United States)

    Tanikawa, Akio; Shinkai, Akira; Miyashita, Tadashi

    2014-11-01

    The evolutionary process of the unique web architectures of spiders of the sub-family Cyrtarachninae, which includes the triangular web weaver, bolas spider, and webless spider, is thought to be derived from reduction of orbicular 'spanning-thread webs' resembling ordinal orb webs. A molecular phylogenetic analysis was conducted to explore this hypothesis using orbicular web spiders Cyrtarachne, Paraplectana, Poecilopachys, triangular web spider Pasilobus, bolas spiders Ordgarius and Mastophora, and webless spider Celaenia. The phylogeny inferred from partial sequences of mt-COI, nuclear 18S-rRNA and 28S-rRNA showed that the common ancestor of these spiders diverged into two clades: a spanning-thread web clade and a bolas or webless clade. This finding suggests that the triangular web evolved by reduction of an orbicular spanning web, but that bolas spiders evolved in the early stage, which does not support the gradual web reduction hypothesis.

  13. That awkward age for butterflies: insights from the age of the butterfly subfamily Nymphalinae (Lepidoptera: Nymphalidae).

    Science.gov (United States)

    Wahlberg, Niklas

    2006-10-01

    The study of the historical biogeography of butterflies has been hampered by a lack of well-resolved phylogenies and a good estimate of the temporal span over which butterflies have evolved. Recently there has been surge of phylogenetic hypotheses for various butterfly groups, but estimating ages of divergence is still in its infancy for this group of insects. The main problem has been the sparse fossil record for butterflies. In this study I have used a surprisingly good fossil record for the subfamily Nymphalinae (Lepidoptera: Nymphalidae) to estimate the ages of diversification of major lineages using Bayesian relaxed clock methods. I have investigated the effects of varying priors on posterior estimates in the analyses. For this data set, it is clear that the prior of the rate of molecular evolution at the ingroup node had the largest effect on the results. Taking this into account, I have been able to arrive at a plausible history of lineage splits, which appears to be correlated with known paleogeological events. The subfamily appears to have diversified soon after the K/T event about 65 million years ago. Several splits are coincident with major paleogeological events, such as the connection of the African and Asian continents about 21 million years ago and the presence of a peninsula of land connecting the current Greater Antilles to the South American continent 35 to 33 million years ago. My results suggest that the age of Nymphalidae is older than the 70 million years speculated to be the age of butterflies as a whole.

  14. Comparative Mitogenomic Analysis of Species Representing Six Subfamilies in the Family Tenebrionidae

    Directory of Open Access Journals (Sweden)

    Hong-Li Zhang

    2016-05-01

    Full Text Available To better understand the architecture and evolution of the mitochondrial genome (mitogenome, mitogenomes of ten specimens representing six subfamilies in Tenebrionidae were selected, and comparative analysis of these mitogenomes was carried out in this study. Ten mitogenomes in this family share a similar gene composition, gene order, nucleotide composition, and codon usage. In addition, our results show that nucleotide bias was strongly influenced by the preference of codon usage for A/T rich codons which significantly correlated with the G + C content of protein coding genes (PCGs. Evolutionary rate analyses reveal that all PCGs have been subjected to a purifying selection, whereas 13 PCGs displayed different evolution rates, among which ATPase subunit 8 (ATP8 showed the highest evolutionary rate. We inferred the secondary structure for all RNA genes of Tenebrio molitor (Te2 and used this as the basis for comparison with the same genes from other Tenebrionidae mitogenomes. Some conserved helices (stems and loops of RNA structures were found in different domains of ribosomal RNAs (rRNAs and the cloverleaf structure of transfer RNAs (tRNAs. With regard to the AT-rich region, we analyzed tandem repeat sequences located in this region and identified some essential elements including T stretches, the consensus motif at the flanking regions of T stretch, and the secondary structure formed by the motif at the 3′ end of T stretch in major strand, which are highly conserved in these species. Furthermore, phylogenetic analyses using mitogenomic data strongly support the relationships among six subfamilies: ((Tenebrionidae incertae sedis + (Diaperinae + Tenebrioninae + (Pimeliinae + Lagriinae, which is consistent with phylogenetic results based on morphological traits.

  15. Sex differences in mouse Transient Receptor Potential Cation Channel, Subfamily M, Member 8 expressing trigeminal ganglion neurons.

    Science.gov (United States)

    Caudle, Robert M; Caudle, Stephanie L; Jenkins, Alan C; Ahn, Andrew H; Neubert, John K

    2017-01-01

    The detection of cool temperatures is thought to be mediated by primary afferent neurons that express the cool temperature sensing protein Transient Receptor Potential Cation Channel, Subfamily M, Member 8 (TRPM8). Using mice, this study tested the hypothesis that sex differences in sensitivity to cool temperatures were mediated by differences in neurons that express TRPM8. Ion currents from TRPM8 expressing trigeminal ganglion (TRG) neurons in females demonstrated larger hyperpolarization-activated cyclic nucleotide-gated currents (Ih) than male neurons at both 30° and 18°C. Additionally, female neurons' voltage gated potassium currents (Ik) were suppressed by cooling, whereas male Ik was not significantly affected. At the holding potential tested (-60mV) TRPM8 currents were not visibly activated in either sex by cooling. Modeling the effect of Ih and Ik on membrane potentials demonstrated that at 30° the membrane potential in both sexes is unstable. At 18°, female TRPM8 TRG neurons develop a large oscillating pattern in their membrane potential, whereas male neurons become highly stable. These findings suggest that the differences in Ih and Ik in the TRPM8 TRG neurons of male and female mice likely leads to greater sensitivity of female mice to the cool temperature. This hypothesis was confirmed in an operant reward/conflict assay. Female mice contacted an 18°C surface for approximately half the time that males contacted the cool surface. At 33° and 10°C male and female mice contacted the stimulus for similar amounts of time. These data suggest that sex differences in the functioning of Ih and Ik in TRPM8 expressing primary afferent neurons leads to differences in cool temperature sensitivity.

  16. Analysis of the grape MYB R2R3 subfamily reveals expanded wine quality-related clades and conserved gene structure organization across Vitis and Arabidopsis genomes

    Directory of Open Access Journals (Sweden)

    Arce-Johnson Patricio

    2008-07-01

    Full Text Available Abstract Background The MYB superfamily constitutes the most abundant group of transcription factors described in plants. Members control processes such as epidermal cell differentiation, stomatal aperture, flavonoid synthesis, cold and drought tolerance and pathogen resistance. No genome-wide characterization of this family has been conducted in a woody species such as grapevine. In addition, previous analysis of the recently released grape genome sequence suggested expansion events of several gene families involved in wine quality. Results We describe and classify 108 members of the grape R2R3 MYB gene subfamily in terms of their genomic gene structures and similarity to their putative Arabidopsis thaliana orthologues. Seven gene models were derived and analyzed in terms of gene expression and their DNA binding domain structures. Despite low overall sequence homology in the C-terminus of all proteins, even in those with similar functions across Arabidopsis and Vitis, highly conserved motif sequences and exon lengths were found. The grape epidermal cell fate clade is expanded when compared with the Arabidopsis and rice MYB subfamilies. Two anthocyanin MYBA related clusters were identified in chromosomes 2 and 14, one of which includes the previously described grape colour locus. Tannin related loci were also detected with eight candidate homologues in chromosomes 4, 9 and 11. Conclusion This genome wide transcription factor analysis in Vitis suggests that clade-specific grape R2R3 MYB genes are expanded while other MYB genes could be well conserved compared to Arabidopsis. MYB gene abundance, homology and orientation within particular loci also suggests that expanded MYB clades conferring quality attributes of grapes and wines, such as colour and astringency, could possess redundant, overlapping and cooperative functions.

  17. Frequency analysis of TRBV subfamily sjTRECs to characterize T-cell reconstitution in acute leukemia patients after allogeneic hematopoietic stem cell transplantation

    Directory of Open Access Journals (Sweden)

    Yang Lijian

    2011-04-01

    Full Text Available Abstract Background Allogeneic hematopoietic stem cell transplantation (allo-HSCT leads to a prolonged state of immunodeficiency and requires reconstitution of normal T-cell immunity. Signal joint T-cell receptor excision DNA circles (sjTRECs are markers of developmental proximity to the thymus that have been used to evaluate thymic function related to T-cell immune reconstitution after HSCT. To assess the proliferative history in different T-cell receptor beta variable region (TRBV subfamilies of T cells after HSCT, expansion of TRBV subfamily-naive T cells was determined by analysis of a series of TRBV-BD1 sjTRECs. Methods sjTRECs levels were detected by real-time quantitative polymerase chain reaction (PCR in peripheral blood mononuclear cells (PBMCs from 43 Chinese acute leukemia patients who underwent allo-HSCT. Twenty-three TRBV-BD1 sjTRECs were amplified by semi-nested PCR. Sixteen age-matched healthy volunteers served as normal controls. Results sjTRECs levels were low or undetectable in the first 6 weeks after allo-HSCT and increased after 8 weeks post HSCT; however, sjTRECs levels at week 20 post-HSCT were still less than normal controls. Frequencies of TRBV subfamily sjTRECs in PBMCs from recipients at week 8 post-HSCT (29.17 ± 20.97% or at week 16 post-HSCT (38.33 ± 9.03% were significantly lower than those in donors (47.92 ± 13.82% or recipients at pre-HSCT (45.83 ± 14.03%. However, frequencies of TRBV subfamily sjTRECs in recipients at week 30 post-HSCT (42.71 ± 21.62% were similar to those in donors and recipients at pre-HSCT. sjTRECs levels in donors had a positive linear correlation with sjTRECs levels in recipients within 8-12 weeks post-HSCT. Patients with acute graft-versus-host disease (GVHD or chronic GVHD had profoundly reduced TRECs levels during the first year post-HSCT. Frequencies of BV22-BD1 sjTRECs and BV23-BD1 sjTRECs in patients with GVHD were significantly lower than those in recipients at pre-HSCT, and the

  18. Clonal expanded TRA and TRB subfamily T cells in peripheral blood from patients with diffuse large B-cell lymphoma.

    Science.gov (United States)

    Tan, Huo; Ye, Jingmei; Luo, Xiaodan; Chen, Shaohua; Yin, Qingsong; Yang, Lijian; Li, Yangqiu

    2010-04-01

    T cell immunodeficiency is a common feature in cancer patients and may be a contributing factor to the initiation and development of the tumor. In order to characterize the immune status in a group of patients with diffuse large B-cell lymphoma (DLBL), the repertoires of T cell receptor alpha and beta variable regions (TRAV and TRBV) were analyzed. The CDR3 of 29 TRAV and 24 TRBV subfamily genes were analyzed in peripheral blood mononuclear cells from six cases with DLBL using RT-PCR and GeneScan technique. Six normal individuals served as controls. Marked restriction of TRBV repertoire was observed in peripheral blood mononuclear cells (PBMCs) from DLBL. Clonal expanded T cells were found frequently in PBMCs from all DLBL patients; the oligoclonality was most frequent in TRAV6, TRAV8, TRAV12, TRAV21, TRAV22 and TRAV25 subfamilies. Similarly, clonally expanded TRBV subfamily T cells were found in all DLBL patients. The oligoclonality was most frequent in TRBV3, TRBV13 and TRBV15 subfamilies, which could be detected in four out of six cases. In conclusion, the frequent and restricted clonal expansion alphabeta(+) T cells were thought to be the specific immune response to lymphoma-associated antigen.

  19. Taxonomic study on the family Mitridae (Mollusca: Gastropoda: Neogastropoda) from the China's seas. Subfamilies: Imbricariinae and Cylindromitrinae

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    Ninteen species of subfamilies Imbricariinae and Cylindromitrinae, family Mitridae, are recorded from the China's seas. Of which, one genus and six species are recorded for the first time from China' s seas, i.e., genus Ziba Adams H and Adams A, Cancilla (Cancilla)carnicolor, Ziba duplilirata, Z. insculpta, Neocancilla circula, Scabricola (Scabricola) desetangsii, Scabricola (Swainsonia) ocellata ocellata.

  20. ROLE OF ATP BINDING CASSETTE SUB-FAMILY MEMBER 2 (ABCG2) IN MOUSE EMBRYONIC STEM CELL DEVELOPMENT.

    Science.gov (United States)

    ATP binding cassette sub-family member 2 (ABCG2), is a member of the ABC transporter superfamily and a principal xenobiotic transporter. ABCG2 is also highly expressed in certain stem cell populations where it is thought to be related to stem cell plasticity, although the role o...

  1. ROLE OF ATP BINDING CASSETTE SUB-FAMILY MEMBER 2 (ABCG2) IN MOUSE EMBRYONIC STEM CELL DEVELOPMENT.

    Science.gov (United States)

    ATP binding cassette sub-family member 2 (ABCG2), is a member of the ABC transporter superfamily and a principal xenobiotic transporter. ABCG2 is also highly expressed in certain stem cell populations where it is thought to be related to stem cell plasticity, although the role o...

  2. Highly conserved salt bridge stabilizes a proteinase K subfamily enzyme, Aqualysin I, from Thermus aquaticus YT-1.

    Science.gov (United States)

    Sakaguchi, Masayoshi; Osaku, Kanae; Maejima, Susumu; Ohno, Nao; Sugahara, Yasusato; Oyama, Fumitaka; Kawakita, Masao

    2014-01-01

    The proteinase K subfamily enzymes, thermophilic Aqualysin I (AQN) from Thermus aquaticus YT-1 and psychrophilic serine protease (VPR) from Vibrio sp. PA-44, have six and seven salt bridges, respectively. To understand the possible significance of salt bridges in the thermal stability of AQN, we prepared mutant proteins in which amino acid residues participating in salt bridges common to proteinase K subfamily members and intrinsic to AQN were replaced to disrupt the bridges one at a time. Disruption of a salt bridge common to proteinase K subfamily enzymes in the D183N mutant resulted in a significant reduction in thermal stability, and a massive change in the content of the secondary structure was observed, even at 70°C, in the circular dichroism (CD) analysis. These results indicate that the common salt bridge Asp183-Arg12 is important in maintaining the conformation of proteinase K subfamily enzymes and suggest the importance of proximity between the regions around Asp183 and the N-terminal region around Arg12. Of the three mutants that lack an AQN intrinsic salt bridge, D212N was more prone to unfolding at 80°C than the wild-type enzyme. Similarly, D17N and E237Q were less thermostable than the wild-type enzyme, although this may be partially due to increased autolysis. The AQN intrinsic salt bridges appear to confer additional thermal stability to this enzyme. These findings will further our understanding of the factors involved in stabilizing protein structure.

  3. Frames of exponentials:lower frame bounds for finite subfamilies, and approximation of the inverse frame operator

    DEFF Research Database (Denmark)

    Christensen, Ole; Lindner, Alexander M

    2001-01-01

    We give lower frame bounds for finite subfamilies of a frame of exponentials {e(i lambdak(.))}k is an element ofZ in L-2(-pi,pi). We also present a method for approximation of the inverse frame operator corresponding to {e(i lambdak(.))}k is an element ofZ, where knowledge of the frame bounds for...

  4. Three new species in the subfamily Eriopeltinae Sulc from Italy (Hemiptera, Coccoidea, Coccidae) with comments on the genus Lecanopsis.

    Science.gov (United States)

    Pellizzari, Giuseppina

    2013-01-01

    Three new coccid species, namely Hadzibejliaspis ferenci Pellizzari n. sp., Lecanopsis sicula Pellizzari n. sp. and L. salvatorei Pellizzari n. sp. are described and illustrated. Identification keys for the genera in the subfamily Eriopeltinae Sulc and to species in the genera Hadzibejliaspis Koteja and Lecanopsis Targioni Tozzetti are provided.

  5. Checklist of the subfamilies Mirinae and Orthotylinae (Hemiptera: Heteroptera: Miridae in western parts of Kerman Province, Iran

    Directory of Open Access Journals (Sweden)

    Mohsen Shamsi

    2014-03-01

    Full Text Available A faunal study was carried out on the subfamilies Mirinae and Orthotylinae (Heteroptera: Miridae from different parts of western Kerman Province on various host plants. In total 16 species belonging to 14 genera were collected and identified from different host plants and localities.

  6. Sea snakes in Australian waters (Serpentes: subfamilies Hydrophiinae and Laticaudinae)—a review with an updated identification key

    DEFF Research Database (Denmark)

    Redsted Rasmussen, Arne; Sanders, Kate Laura; Guinea, Michael L

    2014-01-01

    Sea snakes (Elapidae, subfamilies Hydrophiinae and Laticaudinae) reach high species richness in the South China Sea and in the Australian region; however, most countries in the two regions still lack up-to-date checklists and identification tools for these snakes. We present an updated reviewed...

  7. Mid-Tertiary dispersal, not Gondwanan vicariance explains distribution patterns in the wax palm subfamily (Ceroxyloideae: Arecaceae).

    Science.gov (United States)

    Trénel, Philipp; Gustafsson, Mats H G; Baker, William J; Asmussen-Lange, Conny B; Dransfield, John; Borchsenius, Finn

    2007-10-01

    The Ceroxyloideae is a small but heterogeneous subfamily of palms (Arecaceae, Palmae). It includes a Caribbean lineage (tribe Cyclospathae), a southern hemisphere disjunction (tribe Ceroxyleae), and an amphi-Andean element (tribe Phytelepheae), until recently considered a distinct subfamily (Phytelephantoideae) due to its highly derived morphology. A variety of hypotheses have been proposed to account for the biogeography of the subfamily, involving Gondwanan vicariance, austral interplate dispersal from South America to Australia via Antarctica, Andean orogeny, and Pleistocene refuges. We assessed the systematic classification and biogeography of the group based on a densely sampled phylogeny using >5.5kb of DNA sequences from three plastid and two nuclear genomic regions. The subfamily and each of its three tribes were resolved as monophyletic with high support. Divergence time estimates based on penalized likelihood and Bayesian dating methods indicate that Gondwanan vicariance is highly unlikely as an explanation for basic disjunctions in tribe Ceroxyleae. Alternative explanations include a mid-Tertiary trans-Atlantic/trans-African dispersal track and the "lemurian stepping stones" hypothesis. Austral interplate dispersal of Oraniopsis to Australia could have occurred, but apparently only in the mid-Eocene/early Oligocene interval after global cooling had begun. Our data do not support Pleistocene climatic changes as drivers for speciation in the Andean-centered Phytelepheae as previously proposed. Radiation in this tribe coincides largely with the major uplift of the Andes, favoring Andean orogeny over Pleistocene climatic changes as a possible speciation-promoting factor in this tribe.

  8. Cloning of MASK, a novel member of the mammalian germinal center kinase III subfamily, with apoptosis-inducing properties

    DEFF Research Database (Denmark)

    Dan, Ippeita; Ong, Shao-En; Watanabe, Norinobu M

    2002-01-01

    We have cloned a novel human GCK family kinase that has been designated as MASK (Mst3 and SOK1-related kinase). MASK is widely expressed and encodes a protein of 416 amino acid residues, with an N-terminal kinase domain and a unique C-terminal region. Like other GCK-III subfamily kinases, MASK does...

  9. Australian water mites of the subfamily Notoaturinae Besch (Acari: Hydrachnidia: Aturidae), with the description of 24 new species

    NARCIS (Netherlands)

    H. Smit

    2010-01-01

    New data are presented on the subfamily Notoaturinae from Australia. Twenty-four new species are described: Austraturus aculeatus n. sp., A. canaliculatus n. sp., A. lamingtonensis n. sp., A. longigenitalis n. sp., A. montanus n. sp., A. otwayensis n. sp., A. tasmanicus n. sp., Azugaturus gibberipal

  10. Australian water mites of the subfamily Notoaturinae Besch (Acari: Hydrachnidia: Aturidae), with the description of 24 new species

    NARCIS (Netherlands)

    Smit, H.

    2010-01-01

    New data are presented on the subfamily Notoaturinae from Australia. Twenty-four new species are described: Austraturus aculeatus n. sp., A. canaliculatus n. sp., A. lamingtonensis n. sp., A. longigenitalis n. sp., A. montanus n. sp., A. otwayensis n. sp., A. tasmanicus n. sp., Azugaturus

  11. THE GRK4 SUBFAMILY OF G PROTEIN-COUPLED RECEPTOR KINASES: ALTERNATIVE SPLICING, GENE ORGANIZATION, AND SEQUENCE CONSERVATION

    Science.gov (United States)

    The GRK4 subfamily of G protein-coupled receptor kinases. Alternative splicing, gene organization, and sequence conservation.Premont RT, Macrae AD, Aparicio SA, Kendall HE, Welch JE, Lefkowitz RJ.Department of Medicine, Howard Hughes Medical Institute, Duke Univer...

  12. Whole genome identification, phylogeny and evolution of the cytochrome P450 family 2 (CYP2) sub-families in birds

    DEFF Research Database (Denmark)

    Almeida, Daniela; Maldonado, Emanuel; Khan, Imran

    2016-01-01

    The cytochrome P450 (CYP) superfamily defends organisms from endogenous and noxious environmental compounds, and thus is crucial for survival. However, beyond mammals the molecular evolution of CYP2 subfamilies is poorly understood. Here, we characterized the CYP2 family across 48 novel avian whole...

  13. Sea snakes in Australian waters (Serpentes: subfamilies Hydrophiinae and Laticaudinae)—a review with an updated identification key

    DEFF Research Database (Denmark)

    Redsted Rasmussen, Arne; Sanders, Kate Laura; Guinea, Michael L

    2014-01-01

    Sea snakes (Elapidae, subfamilies Hydrophiinae and Laticaudinae) reach high species richness in the South China Sea and in the Australian region; however, most countries in the two regions still lack up-to-date checklists and identification tools for these snakes. We present an updated reviewed...

  14. The Exiguobacterium sibiricum 255-15 GtfC Enzyme Represents a Novel Glycoside Hydrolase 70 Subfamily of 4,6-α-Glucanotransferase Enzymes.

    Science.gov (United States)

    Gangoiti, Joana; Pijning, Tjaard; Dijkhuizen, Lubbert

    2015-11-20

    The glycoside hydrolase 70 (GH70) family originally was established for glucansucrase enzymes found solely in lactic acid bacteria synthesizing α-glucan polysaccharides from sucrose (e.g., GtfA). In recent years, we have characterized GtfB and related Lactobacillus enzymes as 4,6-α-glucanotransferase enzymes. These GtfB-type enzymes constitute the first GH70 subfamily of enzymes that are unable to act on sucrose as a substrate but are active with maltodextrins and starch, cleave α1→4 linkages, and synthesize linear α1→6-glucan chains. The GtfB disproportionating type of activity results in the conversion of malto-oligosaccharides into isomalto/malto-polysaccharides with a relatively high percentage of α1→6 linkages. This paper reports the identification of the members of a second GH70 subfamily (designated GtfC enzymes) and the characterization of the Exiguobacterium sibiricum 255-15 GtfC enzyme, which is also inactive with sucrose and displays 4,6-α-glucanotransferase activity with malto-oligosaccharides. GtfC differs from GtfB in synthesizing isomalto/malto-oligosaccharides. Biochemically, the GtfB- and GtfC-type enzymes are related, but phylogenetically, they clearly constitute different GH70 subfamilies, displaying only 30% sequence identity. Whereas the GtfB-type enzyme largely has the same domain order as glucansucrases (with α-amylase domains A, B, and C plus domains IV and V), this GtfC-type enzyme differs in the order of these domains and completely lacks domain V. In GtfC, the sequence of conserved regions I to IV of clan GH-H is identical to that in GH13 (I-II-III-IV) but different from that in GH70 (II-III-IV-I because of a circular permutation of the (β/α)8 barrel. The GtfC 4,6-α-glucanotransferase enzymes thus represent structurally and functionally very interesting evolutionary intermediates between α-amylase and glucansucrase enzymes.

  15. iNR-PhysChem: a sequence-based predictor for identifying nuclear receptors and their subfamilies via physical-chemical property matrix.

    Directory of Open Access Journals (Sweden)

    Xuan Xiao

    Full Text Available Nuclear receptors (NRs form a family of ligand-activated transcription factors that regulate a wide variety of biological processes, such as homeostasis, reproduction, development, and metabolism. Human genome contains 48 genes encoding NRs. These receptors have become one of the most important targets for therapeutic drug development. According to their different action mechanisms or functions, NRs have been classified into seven subfamilies. With the avalanche of protein sequences generated in the postgenomic age, we are facing the following challenging problems. Given an uncharacterized protein sequence, how can we identify whether it is a nuclear receptor? If it is, what subfamily it belongs to? To address these problems, we developed a predictor called iNR-PhysChem in which the protein samples were expressed by a novel mode of pseudo amino acid composition (PseAAC whose components were derived from a physical-chemical matrix via a series of auto-covariance and cross-covariance transformations. It was observed that the overall success rate achieved by iNR-PhysChem was over 98% in identifying NRs or non-NRs, and over 92% in identifying NRs among the following seven subfamilies: NR1--thyroid hormone like, NR2--HNF4-like, NR3--estrogen like, NR4--nerve growth factor IB-like, NR5--fushi tarazu-F1 like, NR6--germ cell nuclear factor like, and NR0--knirps like. These rates were derived by the jackknife tests on a stringent benchmark dataset in which none of protein sequences included has ≥60% pairwise sequence identity to any other in a same subset. As a user-friendly web-server, iNR-PhysChem is freely accessible to the public at either http://www.jci-bioinfo.cn/iNR-PhysChem or http://icpr.jci.edu.cn/bioinfo/iNR-PhysChem. Also a step-by-step guide is provided on how to use the web-server to get the desired results without the need to follow the complicated mathematics involved in developing the predictor. It is anticipated that iNR-PhysChem may

  16. The Exiguobacterium sibiricum 255-15 GtfC Enzyme Represents a Novel Glycoside Hydrolase 70 Subfamily of 4,6-α-Glucanotransferase Enzymes

    Science.gov (United States)

    Gangoiti, Joana; Pijning, Tjaard

    2015-01-01

    The glycoside hydrolase 70 (GH70) family originally was established for glucansucrase enzymes found solely in lactic acid bacteria synthesizing α-glucan polysaccharides from sucrose (e.g., GtfA). In recent years, we have characterized GtfB and related Lactobacillus enzymes as 4,6-α-glucanotransferase enzymes. These GtfB-type enzymes constitute the first GH70 subfamily of enzymes that are unable to act on sucrose as a substrate but are active with maltodextrins and starch, cleave α1→4 linkages, and synthesize linear α1→6-glucan chains. The GtfB disproportionating type of activity results in the conversion of malto-oligosaccharides into isomalto/malto-polysaccharides with a relatively high percentage of α1→6 linkages. This paper reports the identification of the members of a second GH70 subfamily (designated GtfC enzymes) and the characterization of the Exiguobacterium sibiricum 255-15 GtfC enzyme, which is also inactive with sucrose and displays 4,6-α-glucanotransferase activity with malto-oligosaccharides. GtfC differs from GtfB in synthesizing isomalto/malto-oligosaccharides. Biochemically, the GtfB- and GtfC-type enzymes are related, but phylogenetically, they clearly constitute different GH70 subfamilies, displaying only 30% sequence identity. Whereas the GtfB-type enzyme largely has the same domain order as glucansucrases (with α-amylase domains A, B, and C plus domains IV and V), this GtfC-type enzyme differs in the order of these domains and completely lacks domain V. In GtfC, the sequence of conserved regions I to IV of clan GH-H is identical to that in GH13 (I-II-III-IV) but different from that in GH70 (II-III-IV-I because of a circular permutation of the (β/α)8 barrel. The GtfC 4,6-α-glucanotransferase enzymes thus represent structurally and functionally very interesting evolutionary intermediates between α-amylase and glucansucrase enzymes. PMID:26590275

  17. Molecular evidence that only two opsin subfamilies, the blue light- (SWS2) and green light-sensitive (RH2), drive color vision in Atlantic cod (Gadus morhua)

    National Research Council Canada - National Science Library

    Valen, Ragnhild; Edvardsen, Rolf Brudvik; Søviknes, Anne Mette; Drivenes, Øyvind; Helvik, Jon Vidar

    2014-01-01

    ... spectra representing UV and red light. Furthermore, we find that Atlantic cod has duplicated paralogs of both blue-sensitive SWS2 and green-sensitive RH2 subfamilies, with members belonging to each subfamily linked in tandem within the genome...

  18. Transient receptor potential cation channel subfamily V member 1 expressing corneal sensory neurons can be subdivided into at least three subpopulations

    Directory of Open Access Journals (Sweden)

    Abdulhakeem eAlamri

    2015-06-01

    Full Text Available The cornea is innervated by 3 main functional classes of sensory neurons: polymodal nociceptors, pure mechano-nociceptors and cold-sensing neurons. Here we explored transient receptor potential cation channel subfamily V member 1 (TRPV1 expression in guinea pig corneal sensory neurons, a widely used molecular marker of polymodal nociceptors. We used retrograde tracing to identify corneal afferent neurons in the trigeminal ganglion and double label in situ hybridization and/or immunohistochemistry to determine their molecular profile. In addition, we used immunohistochemistry to reveal the neurochemistry and structure of TRPV1 expressing nerve endings in the corneal epithelium. Approximately 45% of corneal afferent neurons expressed TRPV1, 28% expressed Piezo2 (a marker of putative pure mechano-nociceptors and 8% expressed the transient receptor potential cation channel subfamily M member 8 (TRPM8; a marker of cold-sensing neurons. There was no co-expression of TRPV1 and Piezo2 in corneal afferent neurons, but 6% of TRPV1 neurons co-expressed TRPM8. The TRPV1 expressing corneal afferent neurons could be divided into 3 subpopulations on the basis of calcitonin gene-related peptide (CGRP and/or or glial cell line-derived neurotrophic factor family receptor alpha3 (GFRα3 co-expression. In the corneal epithelium, the TRPV1 axons that co-expressed CGRP and GFRα3 ended as simple unbranched endings in the wing cell layer. In contrast, those that only co-expressed GFRα3 had ramifying endings that branched and terminated in the squamous cell layer, whereas those that only co-expressed CGRP had simple endings in the basal epithelium. This study shows that the majority of TRPV1 expressing corneal afferent neurons (>90% are likely to be polymodal nociceptors. Furthermore, TRPV1 expressing corneal afferent neurons can be subdivided into specific subpopulations based on their molecular phenotype, nerve terminal morphology and distribution in the corneal

  19. Identification of the Alternative Promoters of the KChIP4 Subfamily

    Institute of Scientific and Technical Information of China (English)

    Xiao-Yun DENG; Jia-Hui XIA; Fang CAI; Kun XIA; Qian PAN; Zhi-Gao LONG; Ling-Qian WU; De-Sheng LIANG; He-Ping DAI; Zhuo-Hua ZHANG

    2005-01-01

    The subfamily of voltage-dependent potassium (Kv) channel interacting protein 4 (KChIP4)is made up of the auxiliary interacting protein of voltage-dependent potassium channels. In this study, the structure of four splicing variants of the human KChIP4 gene was analyzed. Three of the four isoforms of the KChIP4 gene, KChIP4.1, KChIP4.2 and KChIP4.4, were amplified from mouse and human fetal brain tissues by reverse transcription-polymerase chain reaction and then identified. Based on the bioinformatics analysis of the genomic sequences of the gene, we cloned and characterized two promoter fragments from the KChIP4 gene. One was a 325 bp fragment upstream of the 5' end of the KChIP4.1 mRNA sequence and the other was an 818 bp fragment located immediately at the 5' end of the KChIP4.4 variant. Both of them can initiate the transcription of the reporter gene in HT1080 cells and Sprague-Dawley (SD) rat fetal brain neurons, and they contain C+G islands, except typical TATA boxes and CAAT boxes. This shows that the KChIP4 gene expression is regulated by an alternative promoter.

  20. Contribution of transient receptor potential vanilloid subfamily 1 to endothelin-1-induced thermal hyperalgesia.

    Science.gov (United States)

    Kawamata, T; Ji, W; Yamamoto, J; Niiyama, Y; Furuse, S; Namiki, A

    2008-06-26

    Endothelin-1 (ET-1) plays an important role in peripheral pain processing. However, the mechanisms of the nociceptive action of ET-1 have not been fully elucidated. In this study, we investigated the contribution of transient receptor potential vanilloid subfamily 1 (TRPV1) to ET-1-induced thermal hyperalgesia. Intraplantar ET-1-induced thermal hyperalgesia was examined by assessing the paw withdrawal latency to noxious heat stimuli. In electrophysiological study, whole-cell patch-clamp recordings were performed to investigate the interaction of ET-1 and TRPV1 using human embryonic kidney 293 (HEK293) cells expressing endothelin type A receptor (ET(A)) and TRPV1. Intraplantar ET-1 (3, 10 and 30 pmol) produced thermal hyperalgesia in a dose-dependent manner. Thermal hyperalgesia was attenuated by the inhibition of ET(A) and protein kinase C (PKC) but not that of ET(B). ET-1-induced thermal hyperalgesia was significantly attenuated in TRPV1-deficient mice compared with that in wild-type mice. In voltage-clamp experiments, 10 nM capsaicin evoked small inward currents in HEK293 cells expressing TRPV1 and ET(A). In the presence of ET-1, capsaicin produced much larger current responses (Pthermal hyperalgesia.

  1. Biodiversity of Food Species of the Solanaceae Family: A Preliminary Taxonomic Inventory of Subfamily Solanoideae

    Directory of Open Access Journals (Sweden)

    John Samuels

    2015-05-01

    Full Text Available Over the last fifty years there has been a continual reduction in horticultural and agricultural biodiversity of nutritionally important plants, including those of the Solanaceae family. To add to this, the broad range of traditional crops, previously grown on a sustainable scale in some parts of the world, has been replaced by a narrow range of major crops grown as large-scale monocultures. In order to counteract this trend, and to help maintain a broad wealth of genetic resources, conservation is essential. This, in turn, helps to safeguard food security. A taxonomic inventory, covering the diversity of species in a plant group, is an important first step in conservation. The Solanaceae is one of the major plant families providing food species. A survey of the biodiversity, ethnobotany and taxonomy of subfamily Solanoideae was undertaken and is presented here as an inventory of food species. Fifteen genera provide species that are utilised for food across the world. Of these, only four genera contain economically significant cultivated food cropspecies. The majority of these are in the genus Solanum, whilst Capsicum, Physalis and Lycium contribute the remainder of cultivated crop species. These genera and others also comprise species that are semi-cultivated, tolerated as useful weeds, or gathered from the wild.

  2. Out of Africa:Miocene Dispersal, Vicariance, and Extinction within Hyacinthaceae Subfamily Urgineoideae

    Institute of Scientific and Technical Information of China (English)

    Syed Shujait Ali; Martin Pfosser; Wolfgang Wetschnig; Mario MartnezAzorn; Manuel B. Crespo; Yan Yu

    2013-01-01

    Disjunct distribution patterns in plant lineages are usually explained according to three hypotheses:vicariance, geodispersal, and long-distance dispersal. The role of these hypotheses is tested in Urgineoideae (Hyacinthaceae), a subfamily disjunctly distributed in Africa, Madagascar, India, and the Mediterranean region. The potential ancestral range, dispersal routes, and factors responsible for the current distribution in Urgineoideae are investigated using divergence time estimations. Urgineoideae originated in Southern Africa approximately 48.9 Mya. Two independent dispersal events in the Western Mediterranean region possibly occurred during Early Oligocene and Miocene (29.9-8.5 Mya) via Eastern and Northwestern Africa. A dispersal from Northwestern Africa to India could have occurred between 16.3 and 7.6 Mya. Vicariance and extinction events occurred approximately 21.6 Mya. Colonization of Madagascar occurred between 30.6 and 16.6 Mya, after a single transoceanic dispersal event from Southern Africa. The current disjunct distributions of Urgineoideae are not satisfactorily explained by Gondwana fragmentation or dispersal via boreotropical forests, due to the younger divergence time estimates. The flattened winged seeds of Urgineoideae could have played an important role in long-distance dispersal by strong winds and big storms, whereas geodispersal could have also occurred from Southern Africa to Asia and the Mediterranean region via the so-called arid and high-altitude corridors.

  3. Molecular phylogeny and biogeography of the weevil subfamily Platypodinae reveals evolutionarily conserved range patterns.

    Science.gov (United States)

    Jordal, Bjarte H

    2015-11-01

    Platypodinae is a peculiar weevil subfamily of species that cultivate fungi in tunnels excavated in dead wood. Their geographical distribution is generally restricted, with genera confined to a single continent or large island, which provides a useful system for biogeographical research. This study establishes the first detailed molecular phylogeny of the group, with the aim of testing hypotheses on classification, diversification, and biogeography. A phylogeny was reconstructed based on 3648 nucleotides from COI, EF-1α, CAD, ArgK, and 28S. Tree topology was well resolved and indicated a strong correlation with geography, more so than predicted by previous morphology-based classifications. Tesserocerini was paraphyletic, with Notoplatypus as the sister group to a clade consisting of three main lineages of Tesserocerini and the recently evolved Platypodini. Austroplatypus formed the sister group to all remaining Platypodini and hence confirmed its separate status from Platypus. The Indo-Australian genera of Platypodini were strikingly paraphyletic, suggesting that the taxonomy of this tribe needs careful revision. Ancestral-area reconstructions in Lagrange and S-DIVA were ambiguous for nodes roughly older than 80 Ma. More recent events were firmly assessed and involved post-Gondwanan long-distance dispersal. The Neotropics was colonized three times, all from the Afrotropical region, with the latest event less than 25 Ma that included the ancestor of all Neotropical Platypodini. Copyright © 2015 Elsevier Inc. All rights reserved.

  4. Accurate prediction of enzyme subfamily class using an adaptive fuzzy k-nearest neighbor method.

    Science.gov (United States)

    Huang, Wen-Lin; Chen, Hung-Ming; Hwang, Shiow-Fen; Ho, Shinn-Ying

    2007-01-01

    Amphiphilic pseudo-amino acid composition (Am-Pse-AAC) with extra sequence-order information is a useful feature for representing enzymes. This study first utilizes the k-nearest neighbor (k-NN) rule to analyze the distribution of enzymes in the Am-Pse-AAC feature space. This analysis indicates the distributions of multiple classes of enzymes are highly overlapped. To cope with the overlap problem, this study proposes an efficient non-parametric classifier for predicting enzyme subfamily class using an adaptive fuzzy r-nearest neighbor (AFK-NN) method, where k and a fuzzy strength parameter m are adaptively specified. The fuzzy membership values of a query sample Q are dynamically determined according to the position of Q and its weighted distances to the k nearest neighbors. Using the same enzymes of the oxidoreductases family for comparisons, the prediction accuracy of AFK-NN is 76.6%, which is better than those of Support Vector Machine (73.6%), the decision tree method C5.0 (75.4%) and the existing covariant-discriminate algorithm (70.6%) using a jackknife test. To evaluate the generalization ability of AFK-NN, the datasets for all six families of entirely sequenced enzymes are established from the newly updated SWISS-PROT and ENZYME database. The accuracy of AFK-NN on the new large-scale dataset of oxidoreductases family is 83.3%, and the mean accuracy of the six families is 92.1%.

  5. The exodus subfamily of CC chemokines inhibits the proliferation of chronic myelogenous leukemia progenitors.

    Science.gov (United States)

    Hromas, R; Cripe, L; Hangoc, G; Cooper, S; Broxmeyer, H E

    2000-02-15

    Chemokines are a family of related proteins that regulate leukocyte infiltration into inflamed tissue and play important roles in disease processes. Among the biologic activities of chemokines is inhibition of proliferation of normal hematopoietic progenitors. However, chemokines that inhibit normal progenitors rarely inhibit proliferation of hematopoietic progenitors from patients with chronic myelogenous leukemia (CML). We and others recently cloned a subfamily of CC chemokines that share similar amino-terminal peptide sequences and a remarkable ability to chemoattract T cells. These chemokines, Exodus-1/LARC/MIP-3alpha, Exodus-2/SLC/6Ckine/TCA4, and Exodus-3/CKbeta11/MIP-3beta, were found to inhibit proliferation of normal human marrow progenitors. The study described here found that these chemokines also inhibited the proliferation of progenitors in every sample of marrow from patients with CML that was tested. This demonstration of consistent inhibition of CML progenitor proliferation makes the 3 Exodus chemokines unique among chemokines. (Blood. 2000;95:1506-1508)

  6. A Suggested New Bacteriophage Genus, “Kp34likevirus”, within the Autographivirinae Subfamily of Podoviridae

    Directory of Open Access Journals (Sweden)

    Harald Eriksson

    2015-04-01

    Full Text Available Klebsiella pneumoniae phages vB_KpnP_SU503 (SU503 and vB_KpnP_SU552A (SU552A are virulent viruses belonging to the Autographivirinae subfamily of Podoviridae that infect and kill multi-resistant K. pneumoniae isolates. Phages SU503 and SU552A show high pairwise nucleotide identity to Klebsiella phages KP34 (NC_013649, F19 (NC_023567 and NTUH-K2044-K1-1 (NC_025418. Bioinformatic analysis of these phage genomes show high conservation of gene arrangement and gene content, conserved catalytically active residues of their RNA polymerase, a common and specific lysis cassette, and form a joint cluster in phylogenetic analysis of their conserved genes. Also, we have performed biological characterization of the burst size, latent period, host specificity (together with KP34 and NTUH-K2044-K1-1, morphology, and structural genes as well as sensitivity testing to various conditions. Based on the analyses of these phages, the creation of a new phage genus is suggested within the Autographivirinae, called “Kp34likevirus” after their type phage, KP34. This genus should encompass the recently genome sequenced Klebsiella phages KP34, SU503, SU552A, F19 and NTUH-K2044-K1-1.

  7. A review of the subfamily Picobiinae Johnston and Kethley, 1973 (Acariformes: Prostigmata: Syringophilidae).

    Science.gov (United States)

    Skoracki, Maciej; Sikora, Bozena; Spicer, Greg S

    2016-05-19

    The fauna of quill mites of the subfamily Picobiinae Johnston and Kethley, 1973 (Acariformes: Cheyletoidea: Syringophilidae) is comprehensively revised. All of 78 known species, which are grouped into 11 genera, are examined and diagnosed or redescribed. Data on picobiine hosts and distribution are summarized, including new host and locality records. The following new species are described: Charadriineopicobia apricaria sp. nov. ex Pluvialis apricaria (Linnaeus) (Charadriiformes: Charadriidae) from France, Neopicobia pari sp. nov. ex Periparus venustulus Swinhoe (type host) (Passeriformes: Paridae) from China, Parus major Linnaeus (Paridae) from Macedonia and Finland, and Poecile varius Temminck and Schlegel (Paridae) from Japan, Picobia magellani sp. nov. ex Scytalopus magellanicus (Gmelin) (Passeriformes: Rhinocryptidae) from Colombia, Picobia lonchura sp. nov. ex Lonchura leucogastra (Blyth) (Passeriformes: Estrildidae) from Indonesia, Picobia makoli sp. nov. ex Xiphocolaptes promeropirhynchus (Lesson) (Passeriformes: Furnariidae) from Colombia. The species Picobia polonica Skoracki, Magowski and Dabert, 2001 syn. nov. is a junior synonym of C. khulkhaskhani Kivganov and Sharafat, 1995. The following new combinations are proposed: Neopicobia ictericus (Skoracki and Glowska, 2010) comb. nov., Rafapicobia brotogeris (Fain, Bochkov and Mironov, 2000) comb. nov., and Rafapicobia ramphastos (Fain, Bochkov and Mironov, 2000) comb. nov. Keys to the all picobiine genera and species are presented, along with a check-list of picobiine species and their hosts.

  8. Crusticorallina gen. nov., a nongeniculate genus in the subfamily Corallinoideae (Corallinales, Rhodophyta).

    Science.gov (United States)

    Hind, Katharine R; Gabrielson, Paul W; P Jensen, Cassandra; Martone, Patrick T

    2016-12-01

    Molecular phylogenetic analyses of 18S rDNA (SSU) gene sequences confirm the placement of Crusticorallina gen. nov. in Corallinoideae, the first nongeniculate genus in an otherwise geniculate subfamily. Crusticorallina is distinguished from all other coralline genera by the following suite of morpho-anatomical characters: (i) sunken, uniporate gametangial and bi/tetrasporangial conceptacles, (ii) cells linked by cell fusions, not secondary pit connections, (iii) an epithallus of 1 or 2 cell layers, (iv) a hypothallus that occupies 50% or more of the total thallus thickness, (v) elongate meristematic cells, and (vi) trichocytes absent. Four species are recognized based on rbcL, psbA and COI-5P sequences, C. painei sp. nov., the generitype, C. adhaerens sp. nov., C. nootkana sp. nov. and C. muricata comb. nov., previously known as Pseudolithophyllum muricatum. Type material of Lithophyllum muricatum, basionym of C. muricata, in TRH comprises at least two taxa, and therefore we accept the previously designated lectotype specimen in UC that we sequenced to confirm its identity. Crusticorallina species are very difficult to distinguish using morpho-anatomical and/or habitat characters, although at specific sites, some species may be distinguished by a combination of morpho-anatomy, habitat and biogeography. The Northeast Pacific now boasts six coralline endemic genera, far more than any other region of the world. © 2016 Phycological Society of America.

  9. Markiana nigripinnis (Perugia, 1891 as a putative member of the subfamily Stevardiinae (Characiformes: Characidae: spermatic evidence

    Directory of Open Access Journals (Sweden)

    Clarianna Martins Baicere-Silva

    Full Text Available The genus Markiana was until recently recognized as incertae sedis in the family Characidae, even though alternative placements for this genus have been advanced since its original description. More recently, it was hypothesized that Markiana nigripinnis is part of a clade informally named the Astyanax clade, indicating the putative close relationship of Markiana with the genus Astyanax. Examination of sperm ultrastructure of representatives of Astyanax and M. nigripinnis shows no evidence for this hypothesized close relationship. Rather, the spermatozoa of M. nigripinnis share characters found in spermatozoa of the non-inseminating members of the subfamily Stevardiinae, such as an angle of nuclear rotation equal to 85º resulting in a lateral position of the double nuclear fossa and flagellum. As with the non-inseminating Stevardiinae, sperm nuclei are also slightly elongate toward the flagellum, the proximal centriole is partially inside the nuclear fossa and anterior and oblique to the distal centriole, and the midpiece is short and strongly asymmetric. Additionally, M. nigripinnis shares with the other members of the Stevardiinae the presence of only four teeth in the inner row of the premaxillary and a short triangular ectopterygoid, which is never more than twice the length of the palatine.

  10. Modulation of the Rat Hepatic Cytochrome P4501A Subfamily Using Biotin Supplementation

    Science.gov (United States)

    Ronquillo-Sánchez, M. D.; Camacho-Carranza, R.; Fernandez-Mejia, C.; Hernández-Ojeda, S.; Elinos-Baez, M.; Espinosa-Aguirre, J. J.

    2013-01-01

    Studies have found that biotin favors glucose and lipid metabolism, and medications containing biotin have been developed. Despite the use of biotin as a pharmacological agent, few studies have addressed toxicity aspects including the possible interaction with cytochrome P450 enzyme family. This study analyzed the effects of pharmacological doses of biotin on the expression and activity of the cytochrome P4501A subfamily involved in the metabolism of xenobiotics. Wistar rats were treated daily with biotin (2 mg/kg, i.p.), while the control groups were treated with saline. All of the rats were sacrificed by cervical dislocation after 1, 3, 5, or 7 days of treatment. CYP1A1 and CYP1A2 mRNAs were modified by biotin while enzyme activity and protein concentration were not affected. The lack of an effect of biotin on CYP1A activity was confirmed using other experimental strategies, including (i) cotreatment of the animals with biotin and a known CYP1A inducer; (ii) the addition of biotin to the reaction mixtures for the measurement of CYP1A1 and CYP1A2 activities; and (iii) the use of an S9 mixture that was prepared from control and biotin-treated rats to analyze the activation of benzo[a]pyrene (BaP) into mutagenic metabolites using the Ames test. The results suggest that biotin does not influence the CYP1A-mediated metabolism of xenobiotics. PMID:23984390

  11. Modulation of the Rat Hepatic Cytochrome P4501A Subfamily Using Biotin Supplementation

    Directory of Open Access Journals (Sweden)

    M. D. Ronquillo-Sánchez

    2013-01-01

    Full Text Available Studies have found that biotin favors glucose and lipid metabolism, and medications containing biotin have been developed. Despite the use of biotin as a pharmacological agent, few studies have addressed toxicity aspects including the possible interaction with cytochrome P450 enzyme family. This study analyzed the effects of pharmacological doses of biotin on the expression and activity of the cytochrome P4501A subfamily involved in the metabolism of xenobiotics. Wistar rats were treated daily with biotin (2 mg/kg, i.p., while the control groups were treated with saline. All of the rats were sacrificed by cervical dislocation after 1, 3, 5, or 7 days of treatment. CYP1A1 and CYP1A2 mRNAs were modified by biotin while enzyme activity and protein concentration were not affected. The lack of an effect of biotin on CYP1A activity was confirmed using other experimental strategies, including (i cotreatment of the animals with biotin and a known CYP1A inducer; (ii the addition of biotin to the reaction mixtures for the measurement of CYP1A1 and CYP1A2 activities; and (iii the use of an S9 mixture that was prepared from control and biotin-treated rats to analyze the activation of benzo[a]pyrene (BaP into mutagenic metabolites using the Ames test. The results suggest that biotin does not influence the CYP1A-mediated metabolism of xenobiotics.

  12. Isolation of two novel ras genes in Dictyostelium discoideum; evidence for a complex, developmentally regulated ras gene subfamily.

    Science.gov (United States)

    Daniel, J; Bush, J; Cardelli, J; Spiegelman, G B; Weeks, G

    1994-02-01

    In Dictyostelium discoideum, three ras genes (rasD, rasG and rasB) and one ras-related gene (rap1) have been previously isolated and characterized, and the deduced amino acid sequence of their predicted protein products share at least 50% sequence identity with the human H-Ras protein. We have now cloned and characterized two additional members of the ras gene subfamily in Dictyostelium, rasC and rasS. These genes are developmentally regulated and unlike the previously isolated Dictyostelium ras genes, maximum levels of their transcripts were detected during aggregation, suggesting that the encoded proteins have distinct functions during aggregation. The rasC cDNA encodes a 189 amino acid protein that is 65% identical to the Dictyostelium RasD and RasG proteins and 56% identical to the human H-Ras protein. The predicted 194 amino acid gene product encoded by rasS is 60% identical to the Dictyostelium RasD and RasG proteins and 54% identical to the human H-Ras protein. Whereas RasD, RasG, RasB and Rap1 are totally conserved in their putative effector domains relative to H-Ras, RasC and RasS have single amino acid substitutions in their effector domains, consistent with the idea that they have unique functions. In RasC, aspartic acid-38 has been replaced by asparagine (D38N), and in RasS, isoleucine-36 has been replaced by leucine (I36L). In addition, both proteins have several differences in the effector-proximal domain, a domain which is believed to play a role in Ras target activation. In RasC, there is a single conservative amino acid change in the canonical sequence of the binding site for the Ras-specific monoclonal antibody Y13-259, and consequently, RasC is less immunoreactive with the antibody than either of the Dictyostelium RasD or RasG proteins. In contrast, RasS, which has three substitutions in the Y13-259 binding site, does not react with the Y13-259 antibody.

  13. Crystal structures of two transcriptional regulators from Bacillus cereus define the conserved structural features of a PadR subfamily.

    Directory of Open Access Journals (Sweden)

    Guntur Fibriansah

    Full Text Available PadR-like transcriptional regulators form a structurally-related family of proteins that control the expression of genes associated with detoxification, virulence and multi-drug resistance in bacteria. Only a few members of this family have been studied by genetic, biochemical and biophysical methods, and their structure/function relationships are still largely undefined. Here, we report the crystal structures of two PadR-like proteins from Bacillus cereus, which we named bcPadR1 and bcPadR2 (products of gene loci BC4206 and BCE3449 in strains ATCC 14579 and ATCC 10987, respectively. BC4206, together with its neighboring gene BC4207, was previously shown to become significantly upregulated in presence of the bacteriocin AS-48. DNA mobility shift assays reveal that bcPadR1 binds to a 250 bp intergenic region containing the putative BC4206-BC4207 promoter sequence, while in-situ expression of bcPadR1 decreases bacteriocin tolerance, together suggesting a role for bcPadR1 as repressor of BC4206-BC4207 transcription. The function of bcPadR2 (48% identical in sequence to bcPadR1 is unknown, but the location of its gene just upstream from genes encoding a putative antibiotic ABC efflux pump, suggests a role in regulating antibiotic resistance. The bcPadR proteins are structurally similar to LmrR, a PadR-like transcription regulator in Lactococcus lactis that controls expression of a multidrug ABC transporter via a mechanism of multidrug binding and induction. Together these proteins define a subfamily of conserved, relatively small PadR proteins characterized by a single C-terminal helix for dimerization. Unlike LmrR, bcPadR1 and bcPadR2 lack a central pore for ligand binding, making it unclear whether the transcriptional regulatory roles of bcPadR1 and bcPadR2 involve direct ligand recognition and induction.

  14. Crystal structures of two transcriptional regulators from Bacillus cereus define the conserved structural features of a PadR subfamily.

    Science.gov (United States)

    Fibriansah, Guntur; Kovács, Ákos T; Pool, Trijntje J; Boonstra, Mirjam; Kuipers, Oscar P; Thunnissen, Andy-Mark W H

    2012-01-01

    PadR-like transcriptional regulators form a structurally-related family of proteins that control the expression of genes associated with detoxification, virulence and multi-drug resistance in bacteria. Only a few members of this family have been studied by genetic, biochemical and biophysical methods, and their structure/function relationships are still largely undefined. Here, we report the crystal structures of two PadR-like proteins from Bacillus cereus, which we named bcPadR1 and bcPadR2 (products of gene loci BC4206 and BCE3449 in strains ATCC 14579 and ATCC 10987, respectively). BC4206, together with its neighboring gene BC4207, was previously shown to become significantly upregulated in presence of the bacteriocin AS-48. DNA mobility shift assays reveal that bcPadR1 binds to a 250 bp intergenic region containing the putative BC4206-BC4207 promoter sequence, while in-situ expression of bcPadR1 decreases bacteriocin tolerance, together suggesting a role for bcPadR1 as repressor of BC4206-BC4207 transcription. The function of bcPadR2 (48% identical in sequence to bcPadR1) is unknown, but the location of its gene just upstream from genes encoding a putative antibiotic ABC efflux pump, suggests a role in regulating antibiotic resistance. The bcPadR proteins are structurally similar to LmrR, a PadR-like transcription regulator in Lactococcus lactis that controls expression of a multidrug ABC transporter via a mechanism of multidrug binding and induction. Together these proteins define a subfamily of conserved, relatively small PadR proteins characterized by a single C-terminal helix for dimerization. Unlike LmrR, bcPadR1 and bcPadR2 lack a central pore for ligand binding, making it unclear whether the transcriptional regulatory roles of bcPadR1 and bcPadR2 involve direct ligand recognition and induction.

  15. The collection of type specimens belonging to the subfamily Pimeliinae (Coleoptera, Tenebrionidae in the Natural Sciences Museum of Barcelona, Spain

    Directory of Open Access Journals (Sweden)

    Viñolas, A.

    2017-04-01

    Full Text Available The type collection of the subfamily Pimeliinae (Coleoptera, Tenebrionidae deposited in the Natural Sciences Museum of Barcelona, Spain, was organised, revised and documented. The collection contains 438 type specimens representing 140 different taxa. Of note is a considerable number of species belonging to a subfamily described by Francesc Español, Maurice Antoine, Zoltán Kaszab and Carlo Koch. In this paper we provide all the available information relating to these type specimens and for all taxa (species or subspecies we give the following information: original and current taxonomic status, original citation of type material, the exact transcription of the original label, and the pres-ervation condition of the specimen. We also discuss the differences between the original descriptions and labels. If a taxonomic change has occurred, the references describing those changes are included at the end of the description.

  16. Aepyosciurinae -- a new subfamily of Sciuridae (Rodentia, Mammalia) from basal loess deposits at the northeastern border of Tibetan Plateau

    Institute of Scientific and Technical Information of China (English)

    2003-01-01

    Aepyosciurinae, a new subfamily of Sciuridae, were found at the base of the early Pleistocene loess deposits in Dongxiang County, Gansu Province. Its unilaterally hypsodont and lophodont cheek teeth are unique among the sciurids so far known all over the world. Certain degree of similarity can be observed between the cheek teeth of the new subfamily and the Anomalurinae living in tropical and subtropical forests in central and western Africa. Aepyosciuris orientalis gen. et sp. nov. might have lived in montaneous woodland or grassland and lived on harder leaves, barks, or even grass. This tends to show that the northeastern border area of the Tibetan Plateau had been lifted considerably high in early Pleistocene (ca. 2 Ma), with drier climate, becoming a suitable habitat for Aepyosciurus orientalis.

  17. Molecular phylogeny of the subfamily Stevardiinae Gill, 1858 (Characiformes: Characidae): classification and the evolution of reproductive traits.

    Science.gov (United States)

    Thomaz, Andréa T; Arcila, Dahiana; Ortí, Guillermo; Malabarba, Luiz R

    2015-07-21

    The subfamily Stevardiinae is a diverse and widely distributed clade of freshwater fishes from South and Central America, commonly known as "tetras" (Characidae). The group was named "clade A" when first proposed as a monophyletic unit of Characidae and later designated as a subfamily. Stevardiinae includes 48 genera and around 310 valid species with many species presenting inseminating reproductive strategy. No global hypothesis of relationships is available for this group and currently many genera are listed as incertae sedis or are suspected to be non-monophyletic. We present a molecular phylogeny with the largest number of stevardiine species analyzed so far, including 355 samples representing 153 putative species distributed in 32 genera, to test the group's monophyly and internal relationships. The phylogeny was inferred using DNA sequence data from seven gene fragments (mtDNA: 12S, 16S and COI; nuclear: RAG1, RAG2, MYH6 and PTR). The results support the Stevardiinae as a monophyletic group and a detailed hypothesis of the internal relationships for this subfamily. A revised classification based on the molecular phylogeny is proposed that includes seven tribes and also defines monophyletic genera, including a resurrected genus Eretmobrycon, and new definitions for Diapoma, Hemibrycon, Bryconamericus sensu stricto, and Knodus sensu stricto, placing some small genera as junior synonyms. Inseminating species are distributed in several clades suggesting that reproductive strategy is evolutionarily labile in this group of fishes.

  18. Type 2 diabetes - Tuberculosis co-morbidity is associated with diminished circulating levels of IL-20 subfamily of cytokines.

    Science.gov (United States)

    Kumar, Nathella Pavan; Banurekha, Vaithilingam V; Nair, Dina; Kumaran, Paul; Dolla, Chandra Kumar; Babu, Subash

    2015-12-01

    IL-20 subfamily of cytokines play an important role in both host defense mechanisms and glucose metabolism. Since, the interaction between tuberculosis (TB) and diabetes (DM) involves both of the above processes, we examined the association of IL-20 subfamily of cytokines in TB-DM co-morbidity. We examined circulating plasma cytokine levels in individuals with active TB with (PTB-DM) or without (PTB) diabetes and also those with latent TB with (LTB-DM) or without (LTB) diabetes. PTB-DM is characterized by diminished circulating levels of IL-19, IL-20, IL-22 and IL-24 but increased levels of IL-10. Similarly, LTB-DM was also characterized by diminished circulating levels of IL-10, IL-19, IL-20 and IL-24 but increased levels of IL-22. Moreover, there was a significant negative correlation of IL-10, IL-19, IL-20, IL-22 and IL-24 levels with hemoglobin A1C (HbA1c) levels in both PTB and/or LTB individuals. Finally, PTB is characterized by diminished levels of IL-19, IL-20, IL-22 and IL-24 in comparison to LTB individuals. Our data reveal that coincident diabetes in either PTB or LTB is characterized by decreased production of the IL-20 subfamily of cytokines and suggest that these cytokines might play an important role in pathogenesis or protection.

  19. The Crystal Structure of Streptococcus pyogenes Uridine Phosphorylase Reveals a Distinct Subfamily of Nucleoside Phosphorylases

    Energy Technology Data Exchange (ETDEWEB)

    Tran, Timothy H.; Christoffersen, S.; Allan, Paula W.; Parker, William B.; Piskur, Jure; Serra, I.; Terreni, M.; Ealick, Steven E. (Cornell); (Pavia); (Lund); (Southern Research)

    2011-09-20

    Uridine phosphorylase (UP), a key enzyme in the pyrimidine salvage pathway, catalyzes the reversible phosphorolysis of uridine or 2'-deoxyuridine to uracil and ribose 1-phosphate or 2'-deoxyribose 1-phosphate. This enzyme belongs to the nucleoside phosphorylase I superfamily whose members show diverse specificity for nucleoside substrates. Phylogenetic analysis shows Streptococcus pyogenes uridine phosphorylase (SpUP) is found in a distinct branch of the pyrimidine subfamily of nucleoside phosphorylases. To further characterize SpUP, we determined the crystal structure in complex with the products, ribose 1-phosphate and uracil, at 1.8 {angstrom} resolution. Like Escherichia coli UP (EcUP), the biological unit of SpUP is a hexamer with an ?/? monomeric fold. A novel feature of the active site is the presence of His169, which structurally aligns with Arg168 of the EcUP structure. A second active site residue, Lys162, is not present in previously determined UP structures and interacts with O2 of uracil. Biochemical studies of wild-type SpUP showed that its substrate specificity is similar to that of EcUP, while EcUP is {approx}7-fold more efficient than SpUP. Biochemical studies of SpUP mutants showed that mutations of His169 reduced activity, while mutation of Lys162 abolished all activity, suggesting that the negative charge in the transition state resides mostly on uracil O2. This is in contrast to EcUP for which transition state stabilization occurs mostly at O4.

  20. Evolutionary relationships among primary endosymbionts of the mealybug subfamily phenacoccinae (hemiptera: Coccoidea: Pseudococcidae).

    Science.gov (United States)

    Gruwell, Matthew E; Hardy, Nate B; Gullan, Penny J; Dittmar, Katharina

    2010-11-01

    Mealybugs (Coccoidea: Pseudococcidae) are sap-sucking plant parasites that harbor bacterial endosymbionts within specialized organs. Previous studies have identified two subfamilies, Pseudococcinae and Phenacoccinae, within mealybugs and determined the primary endosymbionts (P-endosymbionts) of the Pseudococcinae to be Betaproteobacteria ("Candidatus Tremblaya princeps") containing Gammaproteobacteria secondary symbionts. Here, the P-endosymbionts of phenacoccine mealybugs are characterized based on 16S rRNA from the bacteria of 20 species of phenacoccine mealybugs and four outgroup Puto species (Coccoidea: Putoidae) and aligned to more than 100 published 16S rRNA sequences from symbiotic and free-living bacteria. Phylogenetic analyses recovered three separate lineages of bacteria from the Phenacoccinae, and these are considered to be the P-endosymbionts of their respective mealybug hosts, with those from (i) the mealybug genus Rastrococcus belonging to the Bacteroidetes, (ii) the subterranean mealybugs, tribe Rhizoecini, also within Bacteroidetes, in a clade sister to cockroach endosymbionts (Blattabacterium), and (iii) the remaining Phenacoccinae within the Betaproteobacteria, forming a well-supported sister group to "Candidatus Tremblaya princeps." Names are proposed for two strongly supported lineages: "Candidatus Brownia rhizoecola" for P-endosymbionts of Rhizoecini and "Candidatus Tremblaya phenacola" for P-endosymbionts of Phenacoccinae excluding Rastrococcus and Rhizoecini. Rates of nucleotide substitution among lineages of Tremblaya were inferred to be significantly faster than those of free-living Betaproteobacteria. Analyses also recovered a clade of Gammaproteobacteria, sister to the P-endosymbiont lineage of aphids ("Candidatus Buchnera aphidicola"), containing the endosymbionts of Putoidae, the secondary endosymbionts of pseudococcine mealybugs, and the endosymbionts of several other insect groups.

  1. Multilocus molecular phylogeny of the suckermouth armored catfishes (Siluriformes: Loricariidae) with a focus on subfamily Hypostominae.

    Science.gov (United States)

    Lujan, Nathan K; Armbruster, Jonathan W; Lovejoy, Nathan R; López-Fernández, Hernán

    2015-01-01

    The Neotropical catfish family Loricariidae is the fifth most species-rich vertebrate family on Earth, with over 800 valid species. The Hypostominae is its most species-rich, geographically widespread, and ecomorphologically diverse subfamily. Here, we provide a comprehensive molecular phylogenetic reappraisal of genus-level relationships in the Hypostominae based on our sequencing and analysis of two mitochondrial and three nuclear loci (4293bp total). Our most striking large-scale systematic discovery was that the tribe Hypostomini, which has traditionally been recognized as sister to tribe Ancistrini based on morphological data, was nested within Ancistrini. This required recognition of seven additional tribe-level clades: the Chaetostoma Clade, the Pseudancistrus Clade, the Lithoxus Clade, the 'Pseudancistrus' Clade, the Acanthicus Clade, the Hemiancistrus Clade, and the Peckoltia Clade. Results of our analysis, which included type- and non-type species for every valid genus in Hypostominae, support the reevaluation and restriction of several historically problematic genera, including Baryancistrus, Cordylancistrus, Hemiancistrus, and Peckoltia. Much of the deep lineage diversity in Hypostominae is restricted to Guiana Shield and northern Andean drainages, with three tribe-level clades still largely restricted to the Guiana Shield. Of the six geographically widespread clades, a paraphyletic assemblage of three contain lineages restricted to drainages west of the Andes Mountains, suggesting that early diversification of the Hypostominae predated the late Miocene surge in Andean uplift. Our results also highlight examples of trophic ecological diversification and convergence in the Loricariidae, including support for three independent origins of highly similar and globally unique morphological specializations for eating wood. Copyright © 2014 Elsevier Inc. All rights reserved.

  2. Cephalocteinae Mulsant et Rey, 1866 (Hemiptera, Heteroptera), a subfamily of Cydnidae new for the Italian fauna: first record of Cephalocteus scarabaeoides (Fabricius, 1807) from Sardinia.

    Science.gov (United States)

    Fancello, Luca; Cillo, Davide; Bazzato, Erika

    2016-01-25

    Cephalocteus scarabaeoides is recorded from the south-western coast of Sardinia, in sandy habitat (marine dunes near the beach), for the first time. The species and the subfamily are new for the Italian fauna.

  3. Cloning and characterization of PAK5, a novel member of mammalian p21-activated kinase-II subfamily that is predominantly expressed in brain

    DEFF Research Database (Denmark)

    Pandey, A.; Dan, I.; Kristiansen, T.Z.;

    2002-01-01

    activates the JNK kinase pathway but not p38 or ERK pathways. PAK5 transcript is predominantly expressed in brain as revealed by Northern blot and in situ hybridization. The expression pattern of PAK5 is distinct from that of PAK4 and PAK6, suggesting a functional division among PAK-II subfamily kinases......The p21-activated kinase (PAK) family of protein kinases has recently attracted considerable attention as an effector of Rho family of small G proteins and as an upstream regulator of MAPK signalling pathways during cellular events such as re-arrangement of the cytoskeleton and apoptosis. We have...... that PAK5 preferentially binds to CDC42 in the presence of GTP and that CRIB motif is essential for this interaction. PAK5 is a functional protein kinase but unlike PAK-I family kinases (PAK1, 2, and 3), the kinase activity of PAK5 does not seem to require the binding of CDC42. Overexpression of PAK5...

  4. Members of rice plasma membrane intrinsic proteins subfamily are involved in arsenite permeability and tolerance in plants.

    Science.gov (United States)

    Mosa, Kareem A; Kumar, Kundan; Chhikara, Sudesh; Mcdermott, Joseph; Liu, Zijuan; Musante, Craig; White, Jason C; Dhankher, Om Parkash

    2012-12-01

    Rice accumulates high level of arsenic (As) in its edible parts and thus plays an important role in the transfer of As into the food chain. However, the mechanisms of As uptake and its detoxification in rice are not well understood. Recently, members of the Nodulin 26-like intrinsic protein (NIP) subfamily of plant aquaporins were shown to transport arsenite in rice and Arabidopsis. Here we report that members of the rice plasma membrane intrinsic protein (PIP) subfamily are also involved in As tolerance and transport. Based on the homology search with the mammalian AQP9 and yeast Fps1 arsenite transporters, we identified and cloned five rice PIP gene subfamily members. qRT-PCR analysis of PIPs in rice root and shoot tissues revealed a significant down regulation of transcripts encoding OsPIP1;2, OsPIP1;3, OsPIP2;4, OsPIP2;6, and OsPIP2;7 in response to arsenite treatment. Heterologous expression of OsPIP2;4, OsPIP2;6, and OsPIP2;7 in Xenopus laevis oocytes significantly increased the uptake of arsenite. Overexpression of OsPIP2;4, OsPIP2;6, and OsPIP2;7 in Arabidopsis yielded enhanced arsenite tolerance and higher biomass accumulation. Further, these transgenic plants showed no significant accumulation of As in shoot and root tissues in long term uptake assays. Whereas, short duration exposure to arsenite caused both active influx and efflux of As in the roots. The data suggests a bidirectional arsenite permeability of rice PIPs in plants. These rice PIPs genes will be highly useful for engineering important food and biofuel crops for enhanced crop productivity on contaminated soils without increasing the accumulation of toxic As in the biomass or edible tissues.

  5. New species and records of the mite genus Prolistrophorus (Acariformes: Listrophoridae) from rodents of the subfamily Sigmodontinae (Rodentia: Cricetidae).

    Science.gov (United States)

    Bochkov, Andre V; Lareschi, Marcela; Barreto, Mauricio

    2014-10-01

    Six fur-mite species of the genus Prolistrophorus Fain, 1970 (Acariformes: Listrophoridae) were recorded from Central and South American rodents of the subfamily Sigmodontinae (Rodentia: Cricetidae). Among them, Prolistrophorus (Aprolistrophorus) parabidentatus sp. nov. from Akodon azarae from Argentina and Prolistrophorus (Aprolistrophorus) tylomys sp. nov. from Tylomys nudicaudus from Guatemala are described as new for science. New hosts are recorded for the following species: Prolistrophorus (Prolistrophorus) grassii (Radford, 1954) from Zygodontomys brevicauda from Colombia, P. (P.) frontalis (Hirst, 1921) from Oligoryzomys sp. from Argentina, P. (P.) argentinus (Hirst, 1921) from Melanomys caliginosus, Akodon affinis from Colombia and Scapteromys aquaticus from Argentina, Prolistrophorus (Beprolistrophorus) hirstianus Fain, 1973 from Scapteromys aquaticus from Argentina.

  6. Sea snakes in Australian waters (Serpentes: subfamilies Hydrophiinae and Laticaudinae)--a review with an updated identification key.

    Science.gov (United States)

    Rasmussen, Arne Redsted; Sanders, Kate Laura; Guinea, Michael L; Amey, Andrew P

    2014-10-02

    Sea snakes (Elapidae, subfamilies Hydrophiinae and Laticaudinae) reach high species richness in the South China Sea and in the Australian region; however, most countries in the two regions still lack up-to-date checklists and identification tools for these snakes. We present an updated reviewed checklist and a new complete identification key to sea snakes in Australian waters. The identification key includes 29 species documented and 4 possibly occurring taxa and is based mostly on easy-to-use external characters. We find no evidence for breeding populations of Laticauda in Australian waters, but include the genus on the list of possibly occurring taxa. 

  7. Inherited surfactant deficiency due to uniparental disomy of rare mutations in the surfactant protein-B and ATP binding cassette, subfamily A, member 3 genes

    Science.gov (United States)

    Hamvas, Aaron; Nogee, Lawrence M.; Wegner, Daniel J.; DePass, Kelcey; Christodoulou, John; Bennetts, Bruce; McQuade, Leon R.; Gray, Peter H.; Deterding, Robin R.; Carroll, Travis R.; Kammesheidt, Anja; Kasch, Laura M.; Kulkarni, Shashikant; Cole, F. Sessions

    2009-01-01

    Objective To characterize inheritance of homozygous, rare, recessive loss-of-function mutations in the surfactant protein-B (SFTPB) or ATP binding cassette, subfamily A, member 3 (ABCA3) genes in newborns with lethal respiratory failure. Study design We resequenced parents whose infants were homozygous for mutations in SFTPB or ABCA3. For infants with only one heterozygous parent, we performed microsatellite analysis for chromosomes 2 (SFTPB) and 16 (ABCA3). Results We identified one infant homozygous for the c.1549C>GAA mutation (121ins2) in SFTPB for whom only the mother was heterozygous and 3 infants homozygous for mutations in ABCA3 (p.K914R, p.P147L, and c.806_7insGCT) for whom only the fathers were heterozygous. For the SP-B deficient infant, microsatellite markers confirmed maternal heterodisomy with segmental isodisomy. Microsatellite analysis confirmed paternal isodisomy for the three ABCA3 deficient infants. Two ABCA3 deficient infants underwent lung transplantation at 3 and 5 months of age, respectively, and two infants died. None exhibited any non-pulmonary phenotype. Conclusions Uniparental disomy should be suspected in infants with rare homozygous mutations in SFTPB or ABCA3. Confirmation of parental carrier status is important to provide recurrence risk and to monitor expression of other phenotypes that may emerge through reduction to homozygosity of recessive alleles. PMID:19647838

  8. ATP-binding cassette G-subfamily transporter 2 regulates cell cycle progression and asymmetric division in mouse cardiac side population progenitor cells.

    Science.gov (United States)

    Sereti, Konstantina-Ioanna; Oikonomopoulos, Angelos; Unno, Kazumasa; Cao, Xin; Qiu, Yiling; Liao, Ronglih

    2013-01-04

    After cardiac injury, cardiac progenitor cells are acutely reduced and are replenished in part by regulated self-renewal and proliferation, which occurs through symmetric and asymmetric cellular division. Understanding the molecular cues controlling progenitor cell self-renewal and lineage commitment is critical for harnessing these cells for therapeutic regeneration. We previously have found that the cell surface ATP-binding cassette G-subfamily transporter 2 (Abcg2) influences the proliferation of cardiac side population (CSP) progenitor cells, but through unclear mechanisms. To determine the role of Abcg2 on cell cycle progression and mode of division in mouse CSP cells. Herein, using CSP cells isolated from wild-type and Abcg2 knockout mice, we found that Abcg2 regulates G1-S cell cycle transition by fluorescence ubiquitination cell cycle indicators, cell cycle-focused gene expression arrays, and confocal live-cell fluorescent microscopy. Moreover, we found that modulation of cell cycle results in transition from symmetric to asymmetric cellular division in CSP cells lacking Abcg2. Abcg2 modulates CSP cell cycle progression and asymmetric cell division, establishing a mechanistic link between this surface transporter and cardiac progenitor cell function. Greater understanding of progenitor cell biology and, in particular, the regulation of resident progenitor cell homeostasis is vital for guiding the future development of cell-based therapies for cardiac regeneration.

  9. Recognition of two major clades and early diverged groups within the subfamily Cyperoideae (Cyperaceae) including Korean sedges.

    Science.gov (United States)

    Jung, Jongduk; Choi, Hong-Keun

    2013-05-01

    We aim to present phylogenetic major groups within the subfamily Cyperoideae (Cyperaceae) on the basis of three molecular data sets; nuclear ribosomal internal transcribed spacer and 5.8S ribosomal RNA region, the ribulose-1, 5-bisphosphate carboxylase/oxygenase large subunit gene, and trnL intron and trnL-F intergenic spacer. Three molecular data and two combined data sets were used to obtain robust and detailed phylogenetic trees by using maximum parsimony and Bayesian inference, respectively. We analyzed 81 genera and 426 species of Cyperaceae, including Korean species. We suggest one early diverged group (EDGs), and two major clades (FAEC and SDC) within the subfamily Cyperoideae. And the clade EDGs comprises six tribes (Schoeneae, Bisboeckelereae, Sclerieae, Cryptangieae, Trilepideae, and Rhynchosporeae) at the basal nodes of Cyperoideae. The FAEC clade (posterior probability [PP]/bootstrap value [BS] = 1.00/85) comprises four tribes (Fuireneae, Abildgaardieae, Eleocharideae, Cypereae), and the SDC clade (PP/BS = 1.00/86) comprises three tribes (Scirpeae, Dulichieae, Cariceae). These three clades used for phylogenetic groups in our study will be useful for establishing the major lineage of the sedge family. The phylogeny of Korean sedges was also investigated within the whole phylogeny of Cyperaceae. The 20 genera of Korean sedges were placed in 10 tribes forming 14 clades.

  10. Resolution of phylogenetic relationships of the major subfamilies of the Delphacidae (Homoptera: Fulgoroidea) using the mitochondrial ribosomal DNA

    Institute of Scientific and Technical Information of China (English)

    EDDY DIJKSTRA; MICHEL A. SLOTMAN; RORY J. POST

    2006-01-01

    Delphacid relationships from the genus level to the subfamily have been completely resolved (among those taxa examined) using sequence data from the 3' end of the 12S gene. Monophyly of the non-asiracine subfamilies was strongly supported and the asiracine Ugyops was placed in the most basal position of the tree. Support levels for monophyly of the Delphacini increased after weighting transversions more heavily than transitions and after removing the cixiid outgroup from the dataset. Among the Delphacini,Conomelus and Megamelus were more closely related to each other than either was to Chloriona. These results are in agreement with the tree based on morphological characters. However, in contrast to morphological data our results strongly supported a sister group relationship between the Stenocraninae and the Kelisiinae. Although the 12S gene fragment gave some information about the species relationships within Chloriona, neither this fragment nor the 5' end of the 16S gene appear to be very useful for this level. Molecular evolutionary patterns provided evidence that there has been a shift in base composition from T to A during the early evolution of the non-Asiracinae. The non-Asiracinae also had comparatively fast substitution rates and these two observations are possibly correlated. In the 'modern' delphacid Chloriona, the AT content was comparatively low in regions free of constraints but this was not the case for 'non-modern' delphacids. The tRNA for valine has been translocated elsewhere, probably before the Delphacidae and Cixiidae diverged from each other.

  11. Analysis of Comparative Sequence and Genomic Data to Verify Phylogenetic Relationship and Explore a New Subfamily of Bacterial Lipases.

    Directory of Open Access Journals (Sweden)

    Malihe Masomian

    Full Text Available Thermostable and organic solvent-tolerant enzymes have significant potential in a wide range of synthetic reactions in industry due to their inherent stability at high temperatures and their ability to endure harsh organic solvents. In this study, a novel gene encoding a true lipase was isolated by construction of a genomic DNA library of thermophilic Aneurinibacillus thermoaerophilus strain HZ into Escherichia coli plasmid vector. Sequence analysis revealed that HZ lipase had 62% identity to putative lipase from Bacillus pseudomycoides. The closely characterized lipases to the HZ lipase gene are from thermostable Bacillus and Geobacillus lipases belonging to the subfamily I.5 with ≤ 57% identity. The amino acid sequence analysis of HZ lipase determined a conserved pentapeptide containing the active serine, GHSMG and a Ca(2+-binding motif, GCYGSD in the enzyme. Protein structure modeling showed that HZ lipase consisted of an α/β hydrolase fold and a lid domain. Protein sequence alignment, conserved regions analysis, clustal distance matrix and amino acid composition illustrated differences between HZ lipase and other thermostable lipases. Phylogenetic analysis revealed that this lipase represented a new subfamily of family I of bacterial true lipases, classified as family I.9. The HZ lipase was expressed under promoter Plac using IPTG and was characterized. The recombinant enzyme showed optimal activity at 65 °C and retained ≥ 97% activity after incubation at 50 °C for 1h. The HZ lipase was stable in various polar and non-polar organic solvents.

  12. Linked 5S and 45S rDNA sites are highly conserved through the subfamily Aurantioideae (Rutaceae).

    Science.gov (United States)

    Barros E Silva, A E; Dos Santos Soares Filho, W; Guerra, M

    2013-01-01

    Sites of 5S and 45S rDNA are more commonly located on different chromosomes of most angiosperms. Previous investigations have shown that in the subfamily Aurantioideae these sites may appear closely linked (adjacent sites), as in Poncirustrifoliata, or completely isolated, as in some species of Citrus. In the present work, the distribution of rDNA sites was investigated in representatives of 9 genera of Aurantioideae by FISH and CMA banding, aiming to understand the evolution of adjacent sites in the subfamily. A total of 57 rDNA sites were observed, 40 of them being adjacent to each other. All adjacent sites displayed the 45S rDNA array more terminally located. Assuming that the linked 5S-45S rDNA arrangement was the ancestral condition in Aurantioideae, the isolated rDNA sites observed in Clausena excavata,Bergera koenigii, and Fortunella obovata, as well as the complete linkage loss in Citrus maxima and C. medica indicates that unlinked sites arose independently several times in the evolution of the group. The linkage loss may be due to independent dispersion of one or both rDNA sequence families followed by deletion of the corresponding array in the adjacent site. The possible mechanisms behind these events and their occurrence in other groups are discussed.

  13. Crystal structure of Proteus mirabilis lipase, a novel lipase from the Proteus/psychrophilic subfamily of lipase family I.1.

    Directory of Open Access Journals (Sweden)

    Tyler P Korman

    Full Text Available Bacterial lipases from family I.1 and I.2 catalyze the hydrolysis of triacylglycerol between 25-45°C and are used extensively as biocatalysts. The lipase from Proteus mirabilis belongs to the Proteus/psychrophilic subfamily of lipase family I.1 and is a promising catalyst for biodiesel production because it can tolerate high amounts of water in the reaction. Here we present the crystal structure of the Proteus mirabilis lipase, a member of the Proteus/psychrophilic subfamily of I.1lipases. The structure of the Proteus mirabilis lipase was solved in the absence and presence of a bound phosphonate inhibitor. Unexpectedly, both the apo and inhibitor bound forms of P. mirabilis lipase were found to be in a closed conformation. The structure reveals a unique oxyanion hole and a wide active site that is solvent accessible even in the closed conformation. A distinct mechanism for Ca²⁺ coordination may explain how these lipases can fold without specific chaperones.

  14. The first mitochondrial genome for the fishfly subfamily Chauliodinae and implications for the higher phylogeny of Megaloptera.

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    Yuyu Wang

    Full Text Available Megaloptera are a basal holometabolous insect order with larvae exclusively predacious and aquatic. The evolutionary history of Megaloptera attracts great interest because of its antiquity and important systematic status in Holometabola. However, due to the difficulties identifying morphological apomorphies for the group, controversial hypotheses on the monophyly and higher phylogeny of Megaloptera have been proposed. Herein, we describe the complete mitochondrial (mt genome of a fishfly species, Neochauliodes punctatolosus Liu & Yang, 2006, representing the first mt genome of the subfamily Chauliodinae. A phylogenomic analysis was carried out based on the mt genomic sequences of 13 mt protein-coding genes (PCGs and two rRNA genes of nine Neuropterida species, comprising all three orders of Neuropterida and all families and subfamilies of Megaloptera. Both maximum likelihood and Bayesian inference analyses highly support the monophyly of Megaloptera, which was recovered as the sister of Neuroptera. Within Megaloptera, the sister relationship between Corydalinae and Chauliodinae was corroborated. The divergence time estimation suggests that stem lineage of Neuropterida and Coleoptera separated in the Early Permian. The interordinal divergence within Neuropterida might have occurred in the Late Permian.

  15. Testing the reliability of standard and complementary DNA barcodes for the monocot subfamily Alooideae from South Africa.

    Science.gov (United States)

    Daru, Barnabas H; van der Bank, Michelle; Bello, Abubakar; Yessoufou, Kowiyou

    2016-11-23

    Although a standard DNA barcode has been identified for plants, it does not always provide species-level specimen identifications for investigating important ecological questions. In this study, we assessed the species-level discriminatory power of standard (rbcLa + matK) and complementary barcodes (ITS1 and trnH-psbA) within the subfamily Alooideae (Asphodelaceae), a large and recent plant radiation, whose species are important in horticulture yet are threatened. Alooideae has its centre of endemism in southern Africa, with some outlier species occurring elsewhere in Africa and Madagascar. We sampled 360 specimens representing 235 species within all 11 genera of the subfamily. With three distance-based methods, all markers performed poorly for our combined data set, with the highest proportion of correct species-level specimen identifications (30%) found for ITS1. However, when performance was assessed across genera, the discriminatory power varied from 0% for all single markers and combinations in Gasteria to 63% in Haworthiopsis, again for ITS1, suggesting that DNA barcoding success may be related to the evolutionary history of the lineage considered. Although ITS1 could be a good barcode for Haworthiopsis, the generally poor performance of all markers suggests that Alooideae remains a challenge. As species boundaries within Alooideae remain controversial, we call for continued search for suitable markers or the use of genomics approaches to further explore species discrimination in the group.

  16. Relationships among the cyclostome braconid (Hymenoptera: Braconidae) subfamilies inferred from a mitochondrial tRNA gene rearrangement.

    Science.gov (United States)

    Dowton, M

    1999-03-01

    The arrangement of mitochondrial tRNA genes for lysine (K) and aspartate (D) from the junction of the cytochrome oxidase II and ATPase 8 genes was determined in a range of hymenopteran taxa. This indicated that the ancestral arrangement for the order is 'KD', as found in the Diptera (represented by Drosophila and Anopheles) and basal Orthoptera. Most Hymenoptera that evolved after the appearance of parasitism also have the 'KD' arrangement, including noncyclostome braconids. However, most cyclostome braconids have either a 'DK' or a 'DHK' arrangement (where 'H' refers to the tRNA gene for Histidine). In both cases, the aspartate tRNA gene is encoded on the mitochondrial N-strand, rather than the J-strand as is usually the case. This rearrangement identified a monophyletic group not previously recognized, consisting of Rogadinae + Braconinae + Gnamptodontinae + Histeromerinae + Rhyssalinae + Betylobraconinae + Opiinae + Alysiinae. Only one cyclostome subfamily (Doryctinae) retained the 'KD' arrangement, suggesting this to be the most basal of the cyclostome subfamilies, consistent with ectoparasitism being plesiomorphic for the cyclostomes. However, the Aphidiinae also retained the 'KD' arrangement, leaving unresolved the issue of whether they should be included within the cyclostomes.

  17. Identification of a GH110 subfamily of alpha 1,3-galactosidases: novel enzymes for removal of the alpha 3Gal xenotransplantation antigen

    DEFF Research Database (Denmark)

    Liu, Qiyong P; Yuan, Huaiping; Bennett, Eric P

    2008-01-01

    In search of alpha-galactosidases with improved kinetic properties for removal of the immunodominant alpha1,3-linked galactose residues of blood group B antigens, we recently identified a novel prokaryotic family of alpha-galactosidases (CAZy GH110) with highly restricted substrate specificity...... Bacteroides fragilis had exquisite substrate specificity for the branched blood group B structure Galalpha1-3(Fucalpha1-2)Gal, whereas linear oligosaccharides terminated by alpha1,3-linked galactose such as the immunodominant xenotransplantation epitope Galalpha1-3Galbeta1-4GlcNAc did not serve as substrates....... Here we demonstrate the existence of two distinct subfamilies of GH110 in B. fragilis and thetaiotaomicron strains. Members of one subfamily have exclusive specificity for the branched blood group B structures, whereas members of a newly identified subfamily represent linkage specific alpha1...

  18. HCV Proteins and Immunoglobulin Variable Gene (IgV Subfamilies in HCV-Induced Type II Mixed Cryoglobulinemia: A Concurrent Pathogenetic Role

    Directory of Open Access Journals (Sweden)

    Giuseppe Sautto

    2012-01-01

    Full Text Available The association between hepatitis C virus (HCV infection and type II mixed cryoglobulinemia (MCII is well established, but the role played by distinct HCV proteins and by specific components of the anti-HCV humoral immune response remains to be clearly defined. It is widely accepted that HCV drives the expansion of few B-cell clones expressing a restricted pool of selected immunoglobulin variable (IgV gene subfamilies frequently endowed with rheumatoid factor (RF activity. Moreover, the same IgV subfamilies are frequently observed in HCV-transformed malignant B-cell clones occasionally complicating MCII. In this paper, we analyze both the humoral and viral counterparts at the basis of cryoglobulins production in HCV-induced MCII, with particular attention reserved to the single IgV subfamilies most frequently involved.

  19. Biogeography of the leafhopper subfamily Stegelytrinae (Hemiptera: Cicadellidae), based on a cluster analysis of geographical distribution in areas of endemism combined with phylogeny of the subfamily%世界秀头叶蝉亚科生物地理学

    Institute of Scientific and Technical Information of China (English)

    魏琮; 程若琳; 张雅林

    2012-01-01

    Biogeography of the leafhopper subfamily Stegelytrinae Baker is studied based on an analysis of geographical distribution of this subfamily worldwide using a cluster analysis of the zoological distribution of areas of endemism as well as the phylogeny of representatives of this subfamily.Results show that the Stegelytrinae mainly occur in the Oriental Region and in the Mediterranean area of the Palaearctic Region,and this extends to the east side of both Wallace's and Weber's lines.Eleven areas of endemism of this subfamily are recognized.The proportions of endemic taxa in different areas of endemism are generally very high in comparison with other leafhopper groups,but distinct differences could be found among the different areas of endemism of Stegelytrinae.This subfamily is most intensively diversified in the Indochina Peninsula (INCN).This is the stegelytrine distribution center,having the highest biodiversity at both generic and species levels.The dendrogram of endemic areas of Stegelytrinae constructed using cluster analysis of the zoological distribution of Stegelytrinae at generic level shows the endemic areas of Stegelytrinae can be divided into 4 large groups.Relationships among different endemic areas of Stegelytrinae correspond largely to the geologic history of related areas,which indicates that the evolution and vicariance of this subfamily have been closely related to the history of continental drift and climate changes.It is deduced that the presumed monophyletic Stegelytrinae originated in the Oriental Region after North America had separated from Eurasia; this is the case in the monophyletic genera group which is supported by the lateral frontal sutures extending dorsally well beyond the corresponding ocellus.In addition,two expanding traces of the Stegelytrinae are presumed,which remain plausible explanations for the dispersal of Stegelytrinae:(1) New Guinea (and probably (+ Australia)) -Kalimantan-Sumatra-Malay Peninsula-Indochina Peninsula

  20. TCR gene segments from at least one third of V alpha subfamilies rearrange at the delta locus.

    Science.gov (United States)

    Genevée, C; Chung, V; Diu, A; Hercend, T; Triebel, F

    1994-02-01

    Using PCR and an experimentally validated V alpha subfamily-specific oligonucleotide panel (V alpha 1-w29), we have investigated whether the TCR delta chain may increase its combinatorial diversity by using V genes considered as alpha chain-specific. We show that at least 10 distinct human V alpha segments rearrange at the J delta locus, leading to scrambling of the two V gene repertoires. Fifty-five per cent of the V alpha/J delta transcripts characterized here were in frame. The 17 V alpha/C delta chains analysed included an extended CDR3 region with up to 18 aa encoded by the junctional region. In addition, a new J delta segment (J delta 4) has been characterized. Together, these findings demonstrate that combinatorial diversity in the human delta locus is larger than previously thought.

  1. Recent advances regarding the role of ABC subfamily C member 10 (ABCC10) in the efflux of antitumor drugs

    Institute of Scientific and Technical Information of China (English)

    Rishil J. Kathawala; Yi-Jun Wang; Charles R. Ashby Jr; Zhe-Sheng Chen

    2014-01-01

    ABCC10, also known as multidrug-resistant protein 7 (MRP7), is the tenth member of the C subfamily of the ATP-binding cassette (ABC) superfamily. ABCC10 mediates multidrug resistance (MDR) in cancer cells by preventing the intracellular accumulation of certain antitumor drugs. The ABCC10 transporter is a 171-kDa protein that is localized on the basolateral cell membrane. ABCC10 is a broad-specificity transporter of xenobiotics, including antitumor drugs, such as taxanes, epothilone B, vinca alkaloids, and cytarabine, as wel as modulators of the estrogen pathway, such as tamoxifen. In recent years, ABCC10 inhibitors, including cepharanthine, lapatinib, erlotinib, nilotinib, imatinib, sildenafil, and vardenafil, have been reported to overcome ABCC10-mediated MDR. This review discusses some recent and clinically relevant aspects of the ABCC10 drug efflux transporter from the perspective of current chemotherapy, particularly its inhibition by tyrosine kinase inhibitors and phosphodiesterase type 5 inhibitors.

  2. The search for therapeutic bacteriophages uncovers one new subfamily and two new genera of Pseudomonas-infecting Myoviridae.

    Directory of Open Access Journals (Sweden)

    Marine Henry

    Full Text Available In a previous study, six virulent bacteriophages PAK_P1, PAK_P2, PAK_P3, PAK_P4, PAK_P5 and CHA_P1 were evaluated for their in vivo efficacy in treating Pseudomonas aeruginosa infections using a mouse model of lung infection. Here, we show that their genomes are closely related to five other Pseudomonas phages and allow a subdivision into two clades, PAK_P1-like and KPP10-like viruses, based on differences in genome size, %GC and genomic contents, as well as number of tRNAs. These two clades are well delineated, with a mean of 86% and 92% of proteins considered homologous within individual clades, and 25% proteins considered homologous between the two clades. By ESI-MS/MS analysis we determined that their virions are composed of at least 25 different proteins and electron microscopy revealed a morphology identical to the hallmark Salmonella phage Felix O1. A search for additional bacteriophage homologs, using profiles of protein families defined from the analysis of the 11 genomes, identified 10 additional candidates infecting hosts from different species. By carrying out a phylogenetic analysis using these 21 genomes we were able to define a new subfamily of viruses, the Felixounavirinae within the Myoviridae family. The new Felixounavirinae subfamily includes three genera: Felixounalikevirus, PAK_P1likevirus and KPP10likevirus. Sequencing genomes of bacteriophages with therapeutic potential increases the quantity of genomic data on closely related bacteriophages, leading to establishment of new taxonomic clades and the development of strategies for analyzing viral genomes as presented in this article.

  3. A Species-Level Phylogeny of Extant Snakes with Description of a New Colubrid Subfamily and Genus

    Science.gov (United States)

    McKelvy, Alexander D.; Grismer, L. Lee; Bell, Charles D.; Lailvaux, Simon P.

    2016-01-01

    Background With over 3,500 species encompassing a diverse range of morphologies and ecologies, snakes make up 36% of squamate diversity. Despite several attempts at estimating higher-level snake relationships and numerous assessments of generic- or species-level phylogenies, a large-scale species-level phylogeny solely focusing on snakes has not been completed. Here, we provide the largest-yet estimate of the snake tree of life using maximum likelihood on a supermatrix of 1745 taxa (1652 snake species + 7 outgroup taxa) and 9,523 base pairs from 10 loci (5 nuclear, 5 mitochondrial), including previously unsequenced genera (2) and species (61). Results Increased taxon sampling resulted in a phylogeny with a new higher-level topology and corroborate many lower-level relationships, strengthened by high nodal support values (> 85%) down to the species level (73.69% of nodes). Although the majority of families and subfamilies were strongly supported as monophyletic with > 88% support values, some families and numerous genera were paraphyletic, primarily due to limited taxon and loci sampling leading to a sparse supermatrix and minimal sequence overlap between some closely-related taxa. With all rogue taxa and incertae sedis species eliminated, higher-level relationships and support values remained relatively unchanged, except in five problematic clades. Conclusion Our analyses resulted in new topologies at higher- and lower-levels; resolved several previous topological issues; established novel paraphyletic affiliations; designated a new subfamily, Ahaetuliinae, for the genera Ahaetulla, Chrysopelea, Dendrelaphis, and Dryophiops; and appointed Hemerophis (Coluber) zebrinus to a new genus, Mopanveldophis. Although we provide insight into some distinguished problematic nodes, at the deeper phylogenetic scale, resolution of these nodes may require sampling of more slowly-evolving nuclear genes. PMID:27603205

  4. The Search for Therapeutic Bacteriophages Uncovers One New Subfamily and Two New Genera of Pseudomonas-Infecting Myoviridae

    Science.gov (United States)

    Henry, Marine; Bobay, Louis-Marie; Chevallereau, Anne; Saussereau, Emilie; Ceyssens, Pieter-Jan; Debarbieux, Laurent

    2015-01-01

    In a previous study, six virulent bacteriophages PAK_P1, PAK_P2, PAK_P3, PAK_P4, PAK_P5 and CHA_P1 were evaluated for their in vivo efficacy in treating Pseudomonas aeruginosa infections using a mouse model of lung infection. Here, we show that their genomes are closely related to five other Pseudomonas phages and allow a subdivision into two clades, PAK_P1-like and KPP10-like viruses, based on differences in genome size, %GC and genomic contents, as well as number of tRNAs. These two clades are well delineated, with a mean of 86% and 92% of proteins considered homologous within individual clades, and 25% proteins considered homologous between the two clades. By ESI-MS/MS analysis we determined that their virions are composed of at least 25 different proteins and electron microscopy revealed a morphology identical to the hallmark Salmonella phage Felix O1. A search for additional bacteriophage homologs, using profiles of protein families defined from the analysis of the 11 genomes, identified 10 additional candidates infecting hosts from different species. By carrying out a phylogenetic analysis using these 21 genomes we were able to define a new subfamily of viruses, the Felixounavirinae within the Myoviridae family. The new Felixounavirinae subfamily includes three genera: Felixounalikevirus, PAK_P1likevirus and KPP10likevirus. Sequencing genomes of bacteriophages with therapeutic potential increases the quantity of genomic data on closely related bacteriophages, leading to establishment of new taxonomic clades and the development of strategies for analyzing viral genomes as presented in this article. PMID:25629728

  5. Sonorensin: an antimicrobial peptide, belonging to the heterocycloanthracin subfamily of bacteriocins, from a new marine isolate, Bacillus sonorensis MT93.

    Science.gov (United States)

    Chopra, Lipsy; Singh, Gurdeep; Choudhary, Vikas; Sahoo, Debendra K

    2014-05-01

    Marine environments are the greatest fronts of biodiversity, representing a resource of unexploited or unknown microorganisms and new substances having potential applications. Among microbial products, antimicrobial peptides (AMPs) have received great attention recently due to their applications as food preservatives and therapeutic agents. A new marine soil isolate producing an AMP was identified as Bacillus sonorensis based on 16S rRNA gene sequence analysis. It produced an AMP that showed a broad spectrum of activity against both Gram-positive and Gram-negative bacteria. The peptide, named sonorensin, was purified to homogeneity using a combination of chromatographic techniques. The intact molecular mass of the purified peptide, 6,274 Da, as revealed by matrix-assisted laser desorption ionization-time of flight (MALDI-TOF), was in agreement with Tricine-SDS-PAGE analysis. A PCR array of primers was used to identify AMP structural genes, which allowed the successful amplification of the related genes from strain MT93. The putative open reading frame of sonorensin was amplified, cloned into the pET-32a(+) vector, expressed as a thioredoxin (Trx) fusion protein in Escherichia coli, and then purified. Sequence alignment analysis revealed that the bacteriocin being reported could belong to new subfamily of bacteriocins, heterocycloanthracin. The peptide indicated its potential as a biocontrol agent or food antimicrobial agent, due to its antimicrobial activity against bacteria such as Listeria monocytogenes and Staphylococcus aureus. This is the first report of the production, purification, and characterization of wild-type and recombinant bacteriocin by B. sonorensis and the first bacteriocin of the heterocycloanthracin subfamily to be characterized.

  6. In silico cloning and characterization of the TGA (TGACG MOTIF-BINDING FACTOR) transcription factors subfamily in Carica papaya.

    Science.gov (United States)

    Idrovo Espín, Fabio Marcelo; Peraza-Echeverria, Santy; Fuentes, Gabriela; Santamaría, Jorge M

    2012-05-01

    The TGA transcription factors belong to the subfamily of bZIP group D that play a major role in disease resistance and development. Most of the TGA identified in Arabidopsis interact with the master regulator of SAR, NPR1 that controls the expression of PR genes. As a first approach to determine the possible involvement of these transcription factors in papaya defense, we characterized Arabidopsis TGA orthologs from the genome of Carica papaya cv. SunUp. Six orthologs CpTGA1 to CpTGA6, were identified. The predicted CpTGA proteins were highly similar to AtTGA sequences and probably share the same DNA binding properties and transcriptional regulation features. The protein sequences alignment evidenced the presence of conserved domains, characteristic of this group of transcription factors. The phylogeny showed that CpTGA evolved into three different subclades associated with defense and floral development. This is the first report of basal expression patterns assessed by RT-PCR, from the whole subfamily of CpTGA members in different tissues from papaya cv. Maradol mature plants. Overall, CpTGA1, CpTGA3 CpTGA6 and CpTGA4 showed a basal expression in all tissues tested; CpTGA2 expressed strongly in all tissues except in petioles while CpTGA5 expressed only in petals and to a lower extent in petioles. Although more detailed studies in anthers and other floral structures are required, we suggest that CpTGA5 might be tissue-specific, and it might be involved in papaya floral development. On the other hand, we report here for the first time, the expression of the whole family of CpTGA in response to salicylic acid (SA). The expression of CpTGA3, CpTGA4 and CpTGA6 increased in response to SA, what would suggest its involvement in the SAR response in papaya.

  7. A Species-Level Phylogeny of Extant Snakes with Description of a New Colubrid Subfamily and Genus.

    Science.gov (United States)

    Figueroa, Alex; McKelvy, Alexander D; Grismer, L Lee; Bell, Charles D; Lailvaux, Simon P

    2016-01-01

    With over 3,500 species encompassing a diverse range of morphologies and ecologies, snakes make up 36% of squamate diversity. Despite several attempts at estimating higher-level snake relationships and numerous assessments of generic- or species-level phylogenies, a large-scale species-level phylogeny solely focusing on snakes has not been completed. Here, we provide the largest-yet estimate of the snake tree of life using maximum likelihood on a supermatrix of 1745 taxa (1652 snake species + 7 outgroup taxa) and 9,523 base pairs from 10 loci (5 nuclear, 5 mitochondrial), including previously unsequenced genera (2) and species (61). Increased taxon sampling resulted in a phylogeny with a new higher-level topology and corroborate many lower-level relationships, strengthened by high nodal support values (> 85%) down to the species level (73.69% of nodes). Although the majority of families and subfamilies were strongly supported as monophyletic with > 88% support values, some families and numerous genera were paraphyletic, primarily due to limited taxon and loci sampling leading to a sparse supermatrix and minimal sequence overlap between some closely-related taxa. With all rogue taxa and incertae sedis species eliminated, higher-level relationships and support values remained relatively unchanged, except in five problematic clades. Our analyses resulted in new topologies at higher- and lower-levels; resolved several previous topological issues; established novel paraphyletic affiliations; designated a new subfamily, Ahaetuliinae, for the genera Ahaetulla, Chrysopelea, Dendrelaphis, and Dryophiops; and appointed Hemerophis (Coluber) zebrinus to a new genus, Mopanveldophis. Although we provide insight into some distinguished problematic nodes, at the deeper phylogenetic scale, resolution of these nodes may require sampling of more slowly-evolving nuclear genes.

  8. Attraction of tortricid moths of subfamily olethreutinae to field traps baited with dodecadienes.

    Science.gov (United States)

    Chisholm, M D; Reed, D W; Underhill, E W; Palaniswamy, P; Wong, J W

    1985-02-01

    All four geometrical isomers of 7,9- and 8,10-dodecadienes with acetate, alcohol, and aldehyde functional groups were synthesized and field tested. The field survey produced sex attractant lures for 14 insect species. Species in the generaCydia, Grapholita, Eucosma, Pelochrista, Petrova, Phenta, Hedya, and Pseudosciaphila were captured. Defined lures were developed for some of the species captured. Gas chromatographie retention times for all geometrical isomers of 7,9- and 8,10-dodecadienes with acetate, alcohol, and aldehyde functional groups are reported. A study of the isomerization of 8,10-dodecadienyl acetates and aldehydes impregnated in rubber septa is reported.

  9. An early embryonic product of the gene shaggy encodes a serine/threonine protein kinase related to the CDC28/cdc2+ subfamily.

    Science.gov (United States)

    Bourouis, M; Moore, P; Ruel, L; Grau, Y; Heitzler, P; Simpson, P

    1990-09-01

    The product(s) of the gene shaggy (sgg) is required for seemingly unrelated events during the development of Drosophila melanogaster. In embryos, maternal and zygotically derived sgg products are required initially to construct a normal syncytial blastoderm and later for normal segmentation. Furthermore, in mutant animals a process of intercellular communication that is required for the segregation of the neural and epidermal lineage during the formation of the central nervous system and the adult peripheral nervous system is disrupted. Here we describe a transcription unit of approximately 40 kb lying within the cloned chromosomal interval 3B1, and provide evidence that it encodes the sgg+ function. Of seven developmentally regulated transcripts that are partially generated by alternative splicing, two seem to be responsible for early sgg activity. Sequence analysis of corresponding cDNA(s) predicts a protein of 514 amino acids with a canonical catalytic domain found in serine/threonine specific protein kinases, linked to an unusual region rich in Gly, Ala and Ser. A search for homologies as well as a comparative study of the kinase catalytic domain with that of other proteins, revealed that the protein kinase domain of sgg is distantly related to the members of the CDC28/cdc2+ subfamily of protein kinases, all of which play cardinal roles in the regulation of the yeast and mammalian cell cycles. Ubiquitous expression of sgg transcripts was found during embryonic stages. A possible role of the sgg protein in a signal transduction pathway necessary for intercellular communication at different stages of development is discussed.

  10. ATP-binding cassette subfamily B member 1 polymorphisms do not determine cyclosporin exposure, acute rejection or nephrotoxicity after heart transplantation.

    Science.gov (United States)

    Taegtmeyer, Anne B; Breen, Jane B; Smith, John; Burke, Margaret; Leaver, Neil; Pantelidis, Panagiotis; Lyster, Haifa; Yacoub, Magdi H; Barton, Paul J R; Banner, Nicholas R

    2010-01-15

    We hypothesized that genetic variation of ATP-binding cassette subfamily B member 1 (ABCB1) that encodes P-glycoprotein (involved in the uptake of cyclosporin A [CsA]) contributes to trough drug concentrations and thereby to CsA's immunosuppressive and toxic effects. Three hundred thirty-seven adult heart transplant recipients were studied retrospectively. White recipients receiving CsA at month 3 and years 1 to 5 after transplantation (n=192, 168, 156, 130, 95, and 74, respectively) were then studied with respect to ABCB1 genotype or haplotype and CsA disposition. Genotyping was performed using a gel-based polymerase chain reaction method. Dose- and weight-adjusted CsA trough concentrations ([microg/L]/[mg/kg]), time to first endomyocardial biopsy-proven acute rejection episode (grade>or=3A), weaning from steroids at 1 year, and renal function at 1 year posttransplant were measured. An association between dose- and weight-adjusted CsA trough concentrations and ABCB1 haplotypes was found, with 12/1236, 21/2677, 26/3435 CC/GG/CC individuals having significantly higher concentrations than TT/TT/TT individuals at years 1 and 5 (68.9+/-26.9 vs. 54.9+/-19.5 and 70.6+/-35 vs. 50.0+/-12.2 [microg/L]/[mg/kg] Prenal impairment between the genotype or haplotype groups. The association of ABCB1 12/1236, 21/2677, and 26/3435 CC/GG/CC haplotype with increased CsA dose- and weight-adjusted CsA trough concentrations in this group of adult white heart transplant recipients was not consistent over time and had no effect on the incidence of acute rejection or on the development of renal impairment.

  11. Molecular evolution of an Avirulence Homolog (Avh) gene subfamily in Phytophthora ramorum

    Science.gov (United States)

    GossErica M.; Caroline M. Press; Niklaus J. Grünwald

    2008-01-01

    Pathogen effectors can serve a virulence function on behalf of the pathogen or trigger a rapid defense response in resistant hosts. Sequencing of the Phytophthora ramorum genome and subsequent analysis identified a diverse superfamily of approximately 350 genes that are homologous to the four known avirulence genes in plant pathogenic oomycetes and...

  12. Design factors that influence the performance of flight intercept traps for the capture of longhorned beetles (Coleoptera: Cerambycidae) from the subfamilies Lamiinae and Cerambycinae.

    Science.gov (United States)

    Allison, Jeremy D; Bhandari, Basu D; McKenney, Jessica L; Millar, Jocelyn G

    2014-01-01

    In North America, cerambycid beetles can have significant ecological and economic effects on forest ecosystems, and the rate of introduction and/or detection of exotic species is increasing. Detection and survey programs rely on semiochemical-baited intercept traps which are often ineffective for large woodborers like cerambycid beetles. This study examined the effects of flight intercept trap design on the capture of cerambycid beetles in the subfamilies Lamiinae and Cerambycinae. These subfamilies are the two largest in the Cerambycidae and they include many of the most damaging cerambycid pests and species on regulatory watch lists in North America. This study demonstrates that intercept trap design, treatment of trap surfaces with a lubricant, and the type of collection cup all influence the capture of beetles from the subfamilies Lamiinae and Cerambycinae. It also demonstrates that the addition of a large lubricant-treated collar to the bottom funnel of a multiple-funnel trap significantly increases the capture of some Lamiinae. The best trap design for both subfamilies was a lubricant treated multiple-funnel [MF] trap equipped with a wet cup and lubricant treated large collar on the bottom funnel. This design captured between 4 and 14 times more Lamiinae and Cerambycinae than commercially-available MF and panel traps.

  13. Discovery of a living fossil: a new xylastodorine species from New Caledonia (Heteroptera: Thaumastocoridae) and first record of the subfamily from the eastern Hemisphere

    NARCIS (Netherlands)

    Doesburg, van P.H.; Cassis, G.; Monteith, G.B.

    2010-01-01

    A new species belonging to the genus Proxylastodoris Heiss & Popov, 2002, P. kuscheli spec. nov., of the subfamily Xylastodorinae Barber, 1920 (Heteroptera: Thaumastocoridae) is described from New Caledonia. It is the first recent record outside the western Hemisphere of the Xyalstodorinae and is th

  14. New case of lateral asymmetry in fishes: A new subfamily, genus and species of deep water clingfishes from Papua New Guinea, western Pacific Ocean.

    Science.gov (United States)

    Fricke, Ronald; Chen, Jhen-Nien; Chen, Wei-Jen

    2017-01-01

    The unusual clingfish Protogobiesox asymmetricus n. gen, n. sp. is described on the basis of four specimens collected in deep water off the north coast of Papua New Guinea in 2012. The species is characterized by its 9-10 dorsal rays, 8 anal rays, 17-24 pectoral-fin rays, 15 principal caudal-fin rays, 3 gills, third arch with 3 gill rakers, 34-35 total vertebrae, with asymmetrical lateral bending starting behind the skull, bent at an angle of 85°-92°; skull asymmetrical in frontal view; skin naked, surface of head and body without striae; disc without adhesive papillae. A new subfamily Protogobiesocinae is described for this species and Lepadicyathus mendeleevi Prokofiev, 2005, which is redescribed. The new subfamily is compared within the family; keys to the subfamilies of Gobiesocidae and the species within the new subfamily are presented; its phylogenetic relationship to other gobiesocids is inferred based on a multi-locus DNA dataset.

  15. Evolution of C2H2-zinc finger genes and subfamilies in mammals: Species-specific duplication and loss of clusters, genes and effector domains

    Directory of Open Access Journals (Sweden)

    Aubry Muriel

    2008-06-01

    Full Text Available Abstract Background C2H2 zinc finger genes (C2H2-ZNF constitute the largest class of transcription factors in humans and one of the largest gene families in mammals. Often arranged in clusters in the genome, these genes are thought to have undergone a massive expansion in vertebrates, primarily by tandem duplication. However, this view is based on limited datasets restricted to a single chromosome or a specific subset of genes belonging to the large KRAB domain-containing C2H2-ZNF subfamily. Results Here, we present the first comprehensive study of the evolution of the C2H2-ZNF family in mammals. We assembled the complete repertoire of human C2H2-ZNF genes (718 in total, about 70% of which are organized into 81 clusters across all chromosomes. Based on an analysis of their N-terminal effector domains, we identified two new C2H2-ZNF subfamilies encoding genes with a SET or a HOMEO domain. We searched for the syntenic counterparts of the human clusters in other mammals for which complete gene data are available: chimpanzee, mouse, rat and dog. Cross-species comparisons show a large variation in the numbers of C2H2-ZNF genes within homologous mammalian clusters, suggesting differential patterns of evolution. Phylogenetic analysis of selected clusters reveals that the disparity in C2H2-ZNF gene repertoires across mammals not only originates from differential gene duplication but also from gene loss. Further, we discovered variations among orthologs in the number of zinc finger motifs and association of the effector domains, the latter often undergoing sequence degeneration. Combined with phylogenetic studies, physical maps and an analysis of the exon-intron organization of genes from the SCAN and KRAB domains-containing subfamilies, this result suggests that the SCAN subfamily emerged first, followed by the SCAN-KRAB and finally by the KRAB subfamily. Conclusion Our results are in agreement with the "birth and death hypothesis" for the evolution of

  16. Molecular Evidence that Only Two Opsin Subfamilies, the Blue Light- (SWS2) and Green Light-Sensitive (RH2), Drive Color Vision in Atlantic Cod (Gadus morhua): e115436

    National Research Council Canada - National Science Library

    Ragnhild Valen; Rolf Brudvik Edvardsen; Anne Mette Søviknes; Øyvind Drivenes; Jon Vidar Helvik

    2014-01-01

    ... spectra representing UV and red light. Furthermore, we find that Atlantic cod has duplicated paralogs of both blue-sensitive SWS2 and green-sensitive RH2 subfamilies, with members belonging to each subfamily linked in tandem within the genome...

  17. Bayesian mixture modeling using a hybrid sampler with application to protein subfamily identification.

    Science.gov (United States)

    Fong, Youyi; Wakefield, Jon; Rice, Kenneth

    2010-01-01

    Predicting protein function is essential to advancing our knowledge of biological processes. This article is focused on discovering the functional diversification within a protein family. A Bayesian mixture approach is proposed to model a protein family as a mixture of profile hidden Markov models. For a given mixture size, a hybrid Markov chain Monte Carlo sampler comprising both Gibbs sampling steps and hierarchical clustering-based split/merge proposals is used to obtain posterior inference. Inference for mixture size concentrates on comparing the integrated likelihoods. The choice of priors is critical with respect to the performance of the procedure. Through simulation studies, we show that 2 priors that are based on independent data sets allow correct identification of the mixture size, both when the data are homogeneous and when the data are generated from a mixture. We illustrate our method using 2 sets of real protein sequences.

  18. Phylogeny of Bromelioideae (Bromeliaceae) inferred from nuclear and plastid DNA loci reveals the evolution of the tank habit within the subfamily.

    Science.gov (United States)

    Schulte, Katharina; Barfuss, Michael H J; Zizka, Georg

    2009-05-01

    Phylogenetic relationships within subfamily Bromelioideae (Bromeliaceae, Poales) were inferred using DNA sequence data from the low-copy nuclear gene phosphoribulokinase (PRK) and five plastid loci (matK gene, 3'trnK intron, trnL intron, trnL-trnF spacer, atpB-rbcL spacer). The PRK dataset exhibited a considerably higher proportion of potentially informative characters than the plastid dataset (16.9% vs. 3.1%), leading to a higher resolution and improved nodal support of the resulting phylogenies. Bromelia is resolved as sister to the remainder of the subfamily, albeit this relationship receives only weak nodal support. The basal position of Bromelia, as well as Deinacanthon, Greigia, Ochagavia, Fascicularia and Fernseea within the subfamily is corroborated and the remainder of the subfamily forms a highly supported clade (the eu-bromelioids). By the inclusion of nuclear data the sister group position of Fernseea to the eu-bromelioids is now highly supported. Within the eu-bromelioids the resolution of the clade representing the more advanced core bromelioids has increased and further demonstrates the highly problematic generic concept of Aechmea as well as Quesnelia. Moreover, the data were used to examine the evolution of sepal symmetry and the tank habit. Tracing of character transitions onto the molecular phylogeny implies that both characters have undergone only few transitions within the subfamily and thus are not as homoplasious as previously assumed. The character state reconstruction reveals the great importance of the evolution of the tank habit for the diversification of the core bromelioids.

  19. Insect Resistance to Bacillus thuringiensis Toxin Cry2Ab Is Conferred by Mutations in an ABC Transporter Subfamily A Protein.

    Directory of Open Access Journals (Sweden)

    Wee Tek Tay

    2015-11-01

    Full Text Available The use of conventional chemical insecticides and bacterial toxins to control lepidopteran pests of global agriculture has imposed significant selection pressure leading to the rapid evolution of insecticide resistance. Transgenic crops (e.g., cotton expressing the Bt Cry toxins are now used world wide to control these pests, including the highly polyphagous and invasive cotton bollworm Helicoverpa armigera. Since 2004, the Cry2Ab toxin has become widely used for controlling H. armigera, often used in combination with Cry1Ac to delay resistance evolution. Isolation of H. armigera and H. punctigera individuals heterozygous for Cry2Ab resistance in 2002 and 2004, respectively, allowed aspects of Cry2Ab resistance (level, fitness costs, genetic dominance, complementation tests to be characterised in both species. However, the gene identity and genetic changes conferring this resistance were unknown, as was the detailed Cry2Ab mode of action. No cross-resistance to Cry1Ac was observed in mutant lines. Biphasic linkage analysis of a Cry2Ab-resistant H. armigera family followed by exon-primed intron-crossing (EPIC marker mapping and candidate gene sequencing identified three independent resistance-associated INDEL mutations in an ATP-Binding Cassette (ABC transporter gene we named HaABCA2. A deletion mutation was also identified in the H. punctigera homolog from the resistant line. All mutations truncate the ABCA2 protein. Isolation of further Cry2Ab resistance alleles in the same gene from field H. armigera populations indicates unequal resistance allele frequencies and the potential for Bt resistance evolution. Identification of the gene involved in resistance as an ABC transporter of the A subfamily adds to the body of evidence on the crucial role this gene family plays in the mode of action of the Bt Cry toxins. The structural differences between the ABCA2, and that of the C subfamily required for Cry1Ac toxicity, indicate differences in the

  20. Insect Resistance to Bacillus thuringiensis Toxin Cry2Ab Is Conferred by Mutations in an ABC Transporter Subfamily A Protein

    Science.gov (United States)

    Tay, Wee Tek; Mahon, Rod J.; Heckel, David G.; Walsh, Thomas K.; Downes, Sharon; James, William J.; Lee, Sui-Fai; Reineke, Annette; Williams, Adam K.; Gordon, Karl H. J.

    2015-01-01

    The use of conventional chemical insecticides and bacterial toxins to control lepidopteran pests of global agriculture has imposed significant selection pressure leading to the rapid evolution of insecticide resistance. Transgenic crops (e.g., cotton) expressing the Bt Cry toxins are now used world wide to control these pests, including the highly polyphagous and invasive cotton bollworm Helicoverpa armigera. Since 2004, the Cry2Ab toxin has become widely used for controlling H. armigera, often used in combination with Cry1Ac to delay resistance evolution. Isolation of H. armigera and H. punctigera individuals heterozygous for Cry2Ab resistance in 2002 and 2004, respectively, allowed aspects of Cry2Ab resistance (level, fitness costs, genetic dominance, complementation tests) to be characterised in both species. However, the gene identity and genetic changes conferring this resistance were unknown, as was the detailed Cry2Ab mode of action. No cross-resistance to Cry1Ac was observed in mutant lines. Biphasic linkage analysis of a Cry2Ab-resistant H. armigera family followed by exon-primed intron-crossing (EPIC) marker mapping and candidate gene sequencing identified three independent resistance-associated INDEL mutations in an ATP-Binding Cassette (ABC) transporter gene we named HaABCA2. A deletion mutation was also identified in the H. punctigera homolog from the resistant line. All mutations truncate the ABCA2 protein. Isolation of further Cry2Ab resistance alleles in the same gene from field H. armigera populations indicates unequal resistance allele frequencies and the potential for Bt resistance evolution. Identification of the gene involved in resistance as an ABC transporter of the A subfamily adds to the body of evidence on the crucial role this gene family plays in the mode of action of the Bt Cry toxins. The structural differences between the ABCA2, and that of the C subfamily required for Cry1Ac toxicity, indicate differences in the detailed mode

  1. Characterization of new transposable element sub-families from white clover (Trifolium repens) using PCR amplification.

    Science.gov (United States)

    Becker, Kailey E; Thomas, Mary C; Martini, Samer; Shuipys, Tautvydas; Didorchuk, Volodymyr; Shanker, Rachyl M; Laten, Howard M

    2016-10-01

    Transposable elements (TEs) dominate the landscapes of most plant and animal genomes. Once considered junk DNA and genetic parasites, these interspersed, repetitive DNA elements are now known to play major roles in both genetic and epigenetic processes that sponsor genome variation and regulate gene expression. Knowledge of TE consensus sequences from elements in species whose genomes have not been sequenced is limited, and the individual TEs that are encountered in clones or short-reads rarely represent potentially canonical, let alone, functional representatives. In this study, we queried the Repbase database with eight BAC clones from white clover (Trifolium repens), identified a large number of candidate TEs, and used polymerase chain reaction and Sanger sequencing to create consensus sequences for three new TE families. The results show that TE family consensus sequences can be obtained experimentally in species for which just a single, full-length member of a TE family has been sequenced.

  2. The complex evolutionary dynamics of Hsp70s: a genomic and functional perspective.

    Science.gov (United States)

    Kominek, Jacek; Marszalek, Jaroslaw; Neuvéglise, Cécile; Craig, Elizabeth A; Williams, Barry L

    2013-01-01

    Hsp70 molecular chaperones are ubiquitous. By preventing aggregation, promoting folding, and regulating degradation, Hsp70s are major factors in the ability of cells to maintain proteostasis. Despite a wealth of functional information, little is understood about the evolutionary dynamics of Hsp70s. We undertook an analysis of Hsp70s in the fungal clade Ascomycota. Using the well-characterized 14 Hsp70s of Saccharomyces cerevisiae, we identified 491 orthologs from 53 genomes. Saccharomyces cerevisiae Hsp70s fall into seven subfamilies: four canonical-type Hsp70 chaperones (SSA, SSB, KAR, and SSC) and three atypical Hsp70s (SSE, SSZ, and LHS) that play regulatory roles, modulating the activity of canonical Hsp70 partners. Each of the 53 surveyed genomes harbored at least one member of each subfamily, and thus establishing these seven Hsp70s as units of function and evolution. Genomes of some species contained only one member of each subfamily that is only seven Hsp70s. Overall, members of each subfamily formed a monophyletic group, suggesting that each diversified from their corresponding ancestral gene present in the common ancestor of all surveyed species. However, the pattern of evolution varied across subfamilies. At one extreme, members of the SSB subfamily evolved under concerted evolution. At the other extreme, SSA and SSC subfamilies exhibited a high degree of copy number dynamics, consistent with a birth-death mode of evolution. KAR, SSE, SSZ, and LHS subfamilies evolved in a simple divergent mode with little copy number dynamics. Together, our data revealed that the evolutionary history of this highly conserved and ubiquitous protein family was surprising complex and dynamic.

  3. Subfamily-specific adaptations in the structures of two penicillin-binding proteins from Mycobacterium tuberculosis.

    Directory of Open Access Journals (Sweden)

    Daniil M Prigozhin

    Full Text Available Beta-lactam antibiotics target penicillin-binding proteins including several enzyme classes essential for bacterial cell-wall homeostasis. To better understand the functional and inhibitor-binding specificities of penicillin-binding proteins from the pathogen, Mycobacterium tuberculosis, we carried out structural and phylogenetic analysis of two predicted D,D-carboxypeptidases, Rv2911 and Rv3330. Optimization of Rv2911 for crystallization using directed evolution and the GFP folding reporter method yielded a soluble quadruple mutant. Structures of optimized Rv2911 bound to phenylmethylsulfonyl fluoride and Rv3330 bound to meropenem show that, in contrast to the nonspecific inhibitor, meropenem forms an extended interaction with the enzyme along a conserved surface. Phylogenetic analysis shows that Rv2911 and Rv3330 belong to different clades that emerged in Actinobacteria and are not represented in model organisms such as Escherichia coli and Bacillus subtilis. Clade-specific adaptations allow these enzymes to fulfill distinct physiological roles despite strict conservation of core catalytic residues. The characteristic differences include potential protein-protein interaction surfaces and specificity-determining residues surrounding the catalytic site. Overall, these structural insights lay the groundwork to develop improved beta-lactam therapeutics for tuberculosis.

  4. TP0262 is a modulator of promoter activity of tpr Subfamily II genes of Treponema pallidum ssp. pallidum.

    Science.gov (United States)

    Giacani, Lorenzo; Godornes, Charmie; Puray-Chavez, Maritza; Guerra-Giraldez, Cristina; Tompa, Martin; Lukehart, Sheila A; Centurion-Lara, Arturo

    2009-06-01

    Transcriptional regulation in Treponema pallidum ssp. pallidum is poorly understood, primarily because this organism cannot be cultivated in vitro or genetically manipulated. We have recently shown a phase variation mechanism controlling transcription initiation of Subfamily II tpr (T. pallidumrepeat) genes (tprE, tprG and tprJ), a group of virulence factor candidates. Furthermore, the same study suggested that additional mechanisms might influence the level of transcription of these tprs. The T. pallidum genome sequence has revealed a few open reading frames with similarity to known bacterial transcription factors, including four catabolite activator protein homologues. In this work, sequences matching the Escherichia coli cAMP receptor protein (CRP) binding motif were identified in silico upstream of tprE, tprG and tprJ. Using elecrophoretic mobility shift assay and DNaseI footprinting assay, recombinant TP0262, a T. pallidum CRP homologue, was shown to bind specifically to amplicons obtained from the tpr promoters containing putative CRP binding motifs. Using a heterologous reporter system, binding of TP0262 to these promoters was shown to either increase (tprE and tprJ) or decrease (tprG) tpr promoter activity. This is the first characterization of a T. pallidum transcriptional modulator that influences tpr promoter activity.

  5. Insects of the Subfamily Scolytinae (Insecta: Coleoptera, Curculionidae Collected with Pitfall and Ethanol Traps in Primary Forests of Central Amazonia

    Directory of Open Access Journals (Sweden)

    Raimunda Liege Souza de Abreu

    2012-01-01

    Full Text Available An experiment was conducted in a primary forest area of the Tropical Forest Experimental Station, 45 km from Manaus-Boa Vista Highway, in order to compare the insect fauna of the subfamily Scolytinae, in flight activity and on the ground. Five impact traps of the type Escolitideo/Curitiba, with ethanol baits, were installed at the height of 3 m above the ground, and five pitfall traps were buried in the same area of the above ground traps. The data collections were evaluated through abundance, richness, and Simpson diversity index, and, to compare these data with the pitfalls and the months collection, the ANOVA was used. The Pearson correlation test was also carried out to evaluate the meteorological factors (temperature and rainfall. From the total of 2,910 Scolytinae, 2,341 were captured in pitfall traps representing 80.45% and 569 with Escolitideo/Curitiba traps representing 19.55%. The most abundant species in the collections were Xyleborus volvulus Fabricius and Xyleborus affinis Eichhoff, and this was classified as constant in both habitats. The result of the analysis indicates that the Simpson’s index was high and that the abundance of insects was affected by the types of trap and by the month of collection. The analysis of correlation with meteorological factors showed that only Xyleborus spinulosus species presented significant correlation with temperature.

  6. TP0262 is a modulator of promoter activity of tpr Subfamily II genes of Treponema pallidum subsp. pallidum

    Science.gov (United States)

    Giacani, Lorenzo; Godornes, Charmie; Puray-Chavez, Maritza; Guerra-Giraldez, Cristina; Tompa, Martin; Lukehart, Sheila A.; Centurion-Lara, Arturo

    2009-01-01

    Transcriptional regulation in Treponema pallidum subsp. pallidum is poorly understood, primarily because this organism cannot be cultivated in vitro or genetically manipulated. We have recently shown a phase variation mechanism controlling transcription initiation of Subfamily II tpr (T. pallidum repeat) genes (tprE, tprG, and tprJ), a group of virulence factor candidates. Furthermore, the same study suggested that additional mechanisms might influence the level of transcription of these tprs. The T. pallidum genome sequence has revealed a few open reading frames (ORFs) with similarity to known bacterial transcription factors (TFs), including four catabolite activator protein (CAP) homologs. In this work, sequences matching the E. coli cAMP receptor protein (CRP) binding motif were identified in silico upstream of tprE, tprG, and tprJ. Using elecrophoretic mobility shift assay (EMSA) and DNaseI footprinting assay, recombinant TP0262, a T. pallidum CRP homolog, was shown to bind specifically to amplicons obtained from the tpr promoters containing putative CRP binding motifs. Using a heterologous reporter system, binding of TP0262 to these promoters was shown to either increase (tprE and tprJ) or decrease (tprG) tpr promoter activity. This is the first characterization of a T. pallidum transcriptional modulator which influences tpr promoter activity. PMID:19432808

  7. Overview of the Ferdina-like Goniasteridae (Echinodermata: Asteroidea) including a new subfamily, three new genera and fourteen new species.

    Science.gov (United States)

    Mah, Christopher L

    2017-05-25

    Recent assignment of some goniasterid-like Ophidiasteridae into the Goniasteridae has led to further re-evaluation of other ophidiasterids as possible goniasterids. This led to the discovery of new genera and species supported by a distinctive set of characteristics which support a new subfamily, the Ferdininae, a group originally outlined by Marsh and Price (1991) within the Goniasteridae. The historical Ophidiasteridae is paraphyletic and includes several nominal ophidiasterid genera (e.g., Fromia, Neoferdina, etc.). Newly described material has led to the inclusion of six genera,within this group, of which three, Bathyferdina n. gen., Eosaster n. gen., and Kanakaster n. gen., are newly described. Fourteen new species in five genera are described. This includes Bathyferdina aireyae n. gen., n. sp., Eosaster nadiae n. gen., n. sp., Ferdina mena n. sp., Kanakaster balutensis n. gen., n. sp., Kanakaster convexus n. gen., n. sp., Kanakaster discus n. gen., n. sp., Kanakaster larae n. gen., n. sp., Kanakaster plinthinos n. gen., n. sp., Kanakaster solidus n. gen., n. sp., Neoferdina annae n. sp., Neoferdina antigorum, n. sp., Neoferdina momo, n. sp., Neoferdina oni, n. sp., and Paraferdina plakos, n. sp. Identification keys, synopses, and description of these taxa are included.

  8. Blockade of transient receptor potential cation channel subfamily V member 1 promotes regeneration after sciatic nerve injury

    Institute of Scientific and Technical Information of China (English)

    Fei Ren; Hong Zhang; Chao Qi; Mei-ling Gao; Hong Wang; Xia-qing Li

    2015-01-01

    The transient receptor potential cation channel subfamily V member 1 (TRPV1) provides the sensation of pain (nociception). However, it remains unknown whether TRPV1 is activated after peripheral nerve injury, or whether activation of TRPV1 affects neural regeneration. In the present study, we established rat models of unilateral sciatic nerve crush injury, with or without pretreatment with AMG517 (300 mg/kg), a TRPV1 antagonist, injected subcutaneously into the ipsilateral paw 60 minutes before injury. At 1 and 2 weeks after injury, we performed immuno-lfuorescence staining of the sciatic nerve at the center of injury, at 0.3 cm proximal and distal to the injury site, and in the dorsal root ganglia. Our results showed that Wallerian degeneration occurred distal to the injury site, and neurite outgrowth and Schwann cell regeneration occurred proximal to the injury. The number of regenerating myelinated and unmyelinated nerve clus-ters was greater in the AMG517-pretreated rats than in the vehicle-treated group, most notably 2 weeks after injury. TRPV1 expression in the injured sciatic nerve and ipsilateral dorsal root ganglia was markedly greater than on the contralateral side. Pretreatment with AMG517 blocked this effect. These data indicate that TRPV1 is activated or overexpressed after sciatic nerve crush injury, and that blockade of TRPV1 may accelerate regeneration of the injured sciatic nerve.

  9. Phylogenetic relationships, character evolution, and biogeography of the subfamily Lygosominae (Reptilia: Scincidae) inferred from mitochondrial DNA sequences.

    Science.gov (United States)

    Honda, M; Ota, H; Kobayashi, M; Nabhitabhata, J; Yong, H S; Hikida, T

    2000-06-01

    Phylogenetic relationships among the lygosomine skinks were inferred from 1249 base positions of mitochondrial DNA sequences of 12S and 16S rRNA genes. The monophyly of this subfamily was confirmed and the presence of five distinct infrasubfamilial lineages detected. Of these, the Sphenomorphus group appears to have diverged first, followed by the Lygosoma and Egernia groups in order, leaving the Eugongylus and Mabuya groups as sister groups. Our results did not support monophyly of the Mabuya group sensu lato (i.e., an assemblage of the Lygosoma, Egernia, and Mabuya groups), for which a number of morphological and karyological studies demonstrated a considerable similarity. Our results also contradict the previous hypothesis, formulated on the basis of morphological and immunological data, which argued for the sister relationship between the Egernia and the Eugongylus groups. Morphological and karyological characters used to define the Mabuya group (sensu lato) may actually represent plesiomorphic states. The phylogenetic diversity of lygosomine skinks in the Australian region appears to have increased through multiple colonizations from Southeast Asia.

  10. Differential expression of cytochrome P450 enzymes from the CYP2C subfamily in the human brain.

    Science.gov (United States)

    Booth Depaz, Iris M; Toselli, Francesca; Wilce, Peter A; Gillam, Elizabeth M J

    2015-03-01

    Cytochrome P450 enzymes from the CYP2C subfamily play a prominent role in the metabolic clearance of many drugs. CYP2C enzymes have also been implicated in the metabolism of arachidonic acid to vasoactive epoxyeicosatrienoic acids. CYP2C8, CYP2C9, and CYP2C19 are expressed in the adult liver at significant levels; however, the expression of CYP2C enzymes in extrahepatic tissues such as the brain is less well characterized. Form-specific antibodies to CYP2C9 and CYP2C19 were prepared by affinity purification of antibodies raised to unique peptides. CYP2C9 and CYP2C19 were located in microsomal fractions of all five human brain regions examined, namely the frontal cortex, hippocampus, basal ganglia, amygdala, and cerebellum. Both CYP2C9 and CYP2C19 were detected predominantly within the neuronal soma but with expression extending down axons and dendrites in certain regions. Finally, a comparison of cortex samples from alcoholics and age-matched controls suggested that CYP2C9 expression was increased in alcoholics.

  11. Role for Ribosome-Associated Complex and Stress-Seventy subfamily B (RAC-Ssb) in integral membrane protein translation.

    Science.gov (United States)

    Acosta-Sampson, Ligia; Döring, Kristina; Lin, Yuping; Yu, Vivian Y; Bukau, Bernd; Kramer, Günter; Cate, Jamie H D

    2017-10-02

    Targeting of most integral membrane proteins to the endoplasmic reticulum is controlled by the signal recognition particle (SRP), which recognizes a hydrophobic signal sequence near the protein N-terminus. Proper folding of these proteins is monitored by the unfolded protein response, and involves protein degradation pathways to ensure quality control. Here, we identify a new pathway for quality control of major facilitator superfamily transporters that occurs before the first transmembrane helix--the signal sequence recognized by SRP--is made by the ribosome. Increased rates of translation elongation of the N-terminal sequence of these integral membrane proteins can divert the nascent protein chains to the ribosome-associated complex (RAC) and Stress-Seventy Subfamily B (Ssb) chaperones. We also show that quality control of integral membrane proteins by RAC-Ssb couples translation rate to the unfolded protein response, which has implications for understanding mechanisms underlying human disease and protein production in biotechnology. Copyright © 2017, The American Society for Biochemistry and Molecular Biology.

  12. Regulation of antimicrobial resistance by extracytoplasmic function (ECF) sigma factors.

    Science.gov (United States)

    Woods, Emily C; McBride, Shonna M

    2017-01-30

    Extracytoplasmic function (ECF) sigma factors are a subfamily of σ(70) sigma factors that activate genes involved in stress-response functions. In many bacteria, ECF sigma factors regulate resistance to antimicrobial compounds. This review will summarize the ECF sigma factors that regulate antimicrobial resistance in model organisms and clinically relevant pathogens.

  13. Differential epigenetic regulation of TOX subfamily high mobility group box genes in lung and breast cancers.

    Directory of Open Access Journals (Sweden)

    Mathewos Tessema

    Full Text Available Aberrant cytosine methylation affects regulation of hundreds of genes during cancer development. In this study, a novel aberrantly hypermethylated CpG island in cancer was discovered within the TOX2 promoter. TOX2 was unmethylated in normal cells but 28% lung (n = 190 and 23% breast (n = 80 tumors were methylated. Expression of two novel TOX2 transcripts identified was significantly reduced in primary lung tumors than distant normal lung (p<0.05. These transcripts were silenced in methylated lung and breast cancer cells and 5-Aza-2-deoxycytidine treatment re-expressed both. Extension of these assays to TOX, TOX3, and TOX4 genes that share similar genomic structure and protein homology with TOX2 revealed distinct methylation profiles by smoking status, histology, and cancer type. TOX was almost exclusively methylated in breast (43% than lung (5% cancer, whereas TOX3 was frequently methylated in lung (58% than breast (30% tumors. TOX4 was unmethylated in all samples and showed the highest expression in normal lung. Compared to TOX4, expression of TOX, TOX2 and TOX3 in normal lung was 25, 44, and 88% lower, respectively, supporting the premise that reduced promoter activity confers increased susceptibility to methylation during lung carcinogenesis. Genome-wide assays revealed that siRNA-mediated TOX2 knockdown modulated multiple pathways while TOX3 inactivation targeted neuronal development and function. Although these knockdowns did not result in further phenotypic changes of lung cancer cells in vitro, the impact on tissue remodeling, inflammatory response, and cell differentiation pathways suggest a potential role for TOX2 in modulating tumor microenvironment.

  14. Evolution of developmental regulation in the vertebrate FgfD subfamily.

    Science.gov (United States)

    Jovelin, Richard; Yan, Yi-Lin; He, Xinjun; Catchen, Julian; Amores, Angel; Canestro, Cristian; Yokoi, Hayato; Postlethwait, John H

    2010-01-15

    Fibroblast growth factors (Fgfs) encode small signaling proteins that help regulate embryo patterning. Fgfs fall into seven families, including FgfD. Nonvertebrate chordates have a single FgfD gene; mammals have three (Fgf8, Fgf17, and Fgf18); and teleosts have six (fgf8a, fgf8b, fgf17, fgf18a, fgf18b, and fgf24). What are the evolutionary processes that led to the structural duplication and functional diversification of FgfD genes during vertebrate phylogeny? To study this question, we investigated conserved syntenies, patterns of gene expression, and the distribution of conserved noncoding elements (CNEs) in FgfD genes of stickleback and zebrafish, and compared them with data from cephalochordates, urochordates, and mammals. Genomic analysis suggests that Fgf8, Fgf17, Fgf18, and Fgf24 arose in two rounds of whole genome duplication at the base of the vertebrate radiation; that fgf8 and fgf18 duplications occurred at the base of the teleost radiation; and that Fgf24 is an ohnolog that was lost in the mammalian lineage. Expression analysis suggests that ancestral subfunctions partitioned between gene duplicates and points to the evolution of novel expression domains. Analysis of CNEs, at least some of which are candidate regulatory elements, suggests that ancestral CNEs partitioned between gene duplicates. These results help explain the evolutionary pathways by which the developmentally important family of FgfD molecules arose and the deduced principles that guided FgfD evolution are likely applicable to the evolution of developmental regulation in many vertebrate multigene families.

  15. A QUICK KEY TO THE SUBFAMILIES AND GENERA OF ANTS OF THE SAVANNAH RIVER SITE

    Energy Technology Data Exchange (ETDEWEB)

    Martin, D

    2007-09-04

    This taxonomic key was devised to support development of a Rapid Bioassessment Protocol using ants at the Savannah River Site. The emphasis is on 'rapid' and, because the available keys contained a very large number of genera not known to occur at the Savannah River Site, we found that the available keys were unwieldy. Because these keys contained many more genera than we would ever encounter and because this larger number of genera required more couplets in the key and often required examination of characters that are difficult to assess without higher magnifications (60X or higher), more time was required to process samples. In developing this set of keys I emphasized character states that are easier for nonspecialists to recognize. I recognize that the character sets used may lead to some errors but I believe that the error rate will be small and, for the purpose of rapid bioassessment, this error rate will be acceptable provided that overall sample sizes are adequate. Oliver and Beattie (1996a, 1996b) found that for rapid assessment of biodiversity the same results were found when identifications were done to morphospecies by people with minimal expertise as when the same data sets were identified by subject matter experts. Basset et al. (2004) concluded that it was not as important to correctly identify all species as it was to be sure that the study included as many functional groups as possible. If your study requires high levels of accuracy, it is highly recommended that, when you key out a specimen and have any doubts concerning the identification, you should refer to keys in Bolton (1994) or to the other keys used to develop this area specific taxonomic key.

  16. Checklist of the subfamily Adoncholaiminae Gerlach and Riemann, 1974 (Nematoda: Oncholaimida: Oncholaimidae) of the world: genera, species, distribution, and reference list for taxonomists and ecologists

    Science.gov (United States)

    2016-01-01

    Abstract Background Adoncholaiminae is one of the seven subfamilies in the free-living aquatic nematode family Oncholaimidae. Nematodes in Adoncholaiminae are found from various water environment of the world. However, a checklist of all Adoncholaiminae species including full literature, especially information of experimental (not taxonomic) works, has not been updated for more than 40 years. New information A revised checklist of the subfamily Adoncholaiminae of the world is provided. It contains 31 valid and 13 invalid species names in four genera with synonyms, collection records, and full literature from 1860's to 2015 for each species. A literature survey of total 477 previous papers was conducted in this work, and 362 of them are newly added to checklist. PMID:26929708

  17. Genetic association of aromatic hydrocarbon receptor (AHR) and cytochrome P450, family 1, subfamily A, polypeptide 1 (CYP1A1) polymorphisms with dioxin blood concentrations among pregnant Japanese women

    OpenAIRE

    Kobayashi, Sumitaka; Sata, Fumihiro; Sasaki, Seiko; Ban, Susumu; Miyashita, Chihiro; Okada, Emiko; Limpar, Mariko; Yoshioka, Eiji; Kajiwara, Jumboku; TODAKA, Takashi; Saijo, Yasuaki; Kishi, Reiko

    2013-01-01

    Dioxins are metabolized by cytochrome P450, family 1 (CYP1) via the aromatic hydrocarbon receptor (AHR). We determined whether different blood dioxin concentrations are associated with polymorphisms in AHR (dbSNP ID: rs2066853), AHR repressor (AHRR; rs2292596), CYP1 subfamily A polypeptide 1 (CYP1A1; rs4646903 and rs1048963), CYP1 subfamily A polypeptide 2 (CYP1A2; rs762551), and CYP1 subfamily B polypeptide 1 (CYP1B1; rs1056836) in pregnant Japanese women. These six polymorphisms were detect...

  18. Two new mite species of the subfamily Harpirhynchinae Dubinin, 1957 (Acariformes: Harpirhynchidae), parasites of the passerine birds (Aves: Passeriformes) in Australia and South Asia.

    Science.gov (United States)

    Bochkov, Andre V; Klompen, Hans

    2015-09-01

    Two new mite species of the subfamily Harpirhynchinae Dubinin, 1957 (Acariformes: Harpirhynchidae) are described from passerine birds (Aves: Passeriformes): Harpirhynchoides artamus n. sp. from Artamus fuscus Vieillot (Artamidae) from an unknown locality in South Asia and Neharpyrhynchus domrowi n. sp. from three host species of the family Meliphagidae, Acanthorhynchus tenuirostris (Latham) (type-host) from Australia (New South Walles), Ptiloprora perstriata (De Vis) and Myzomela rosenbergii Schlegel from Papua New Guinea.

  19. Composition and interrelationships of a large Neotropical freshwater fish group, the subfamily Cheirodontinae (Characiformes: Characidae): a case study based on mitochondrial and nuclear DNA sequences.

    Science.gov (United States)

    Mariguela, T C; Ortí, G; Avelino, G S; Abe, K T; Oliveira, C

    2013-07-01

    Characidae is the most species-rich family of freshwater fishes in the order Characiformes, with more than 1000 valid species that correspond to approximately 55% of the order. Few hypotheses about the composition and internal relationships within this family are available and most fail to reach an agreement. Among Characidae, Cheirodontinae is an emblematic group that includes 18 genera (1 fossil) and approximately 60 described species distributed throughout the Neotropical region. The taxonomic and systematic history of Cheirodontinae is complex, and only two hypotheses about the internal relationships in this subfamily have been reported to date. In the present study, we test the composition and relationships of fishes assigned to Cheirodontinae based on a broad taxonomic sample that also includes some characid incertae sedis taxa that were previously considered to be part of Cheirodontinae. We present phylogenetic analyses of a large molecular dataset of mitochondrial and nuclear DNA sequences. Our results reject the monophyly of Cheirodontinae as previously conceived, as well as the tribes Cheirodontini and Compsurini, and the genera Cheirodon, Compsura, Leptagoniates, Macropsobrycon, Odontostilbe, and Serrapinnus. On the basis of these results we propose: (1) the exclusion of Amazonspinther and Spintherobolus from the subfamily Cheirodontinae since they are the sister-group of all remaining Characidae; (2) the removal of Macropsobrycon xinguensis of the genus Macropsobrycon; (3) the removal of Leptagoniates pi of the genus Leptagoniates; (4) the inclusion of Leptagoniates pi in the subfamily Cheirodontinae; (5) the removal of Cheirodon stenodon of the genus Cheirodon and its inclusion in the subfamily Cheirodontinae under a new genus name; (6) the need to revise the polyphyletic genera Compsura, Odontostilbe, and Serrapinnus; and (7) the division of Cheirodontinae in three newly defined monophyletic tribes: Cheirodontini, Compsurini, and Pseudocheirodontini

  20. The expression of T-cell receptor Vβ subfamily in hepatitis B virus-related acute-on-chronic liver failure patients and its clinical significance

    Institute of Scientific and Technical Information of China (English)

    施文娟

    2014-01-01

    Objective To investigate the expression and clinical significance of T-cell receptor(TCR)Vβsubfamily in hepatitis B virus(HBV)-related acute-on-chronic liverfailure(HBV-ACLF)patients.Methods Twenty-eight patients with HBV-ACLF(HBV-ACLF group)and 32patients with chronic hepatitis B flare(CHB-F group),who were treated in The Second People’s Hospital from

  1. Polymorphisms in catechol-O-methyltransferase and cytochrome p450 subfamily 19 genes predispose towards Madurella mycetomatis-induced mycetoma susceptibility.

    Science.gov (United States)

    van de Sande, Wendy W J; Fahal, Ahmed; Tavakol, Mehri; van Belkum, Alex

    2010-11-01

    Mycetoma caused by Madurella mycetomatis is a devastating and neglected disease which primarily affects males. Since this predominance cannot be easily explained by behaviour differences between men and women, other factors, including sex hormones, could be the cause. To monitor for possible deficiencies in hormone synthesis among mycetoma patients, we investigated the types and allele frequencies of the genes encoding for catechol-O-methyltransferase (COMT), cytochrome p450 subfamily 1 (CYP1B1), cytochrome p450 subfamily 17 (CYP17), cytochrome p450 subfamily 19 (CYP19) and hydroxysteroid dehydrogenase 3B (HSD3B). Significant differences in allele distribution were demonstrated for CYP19 (P=0.004) and COMT (P=0.005), as well as gender dimorphism for both CYP19 and COMT polymorphisms. The COMT polymorphism was associated with lesion size. The genotypes obtained for COMT and CYP19 were connected with higher 17β-estradiol production, which was confirmed by significantly elevated serum levels of 17β-estradiol in male patients. In contrast, lowered levels of dehydroepiandrosteron (DHEA) were found in mycetoma patients. The in vitro growth of M. mycetomatis was not influenced by 17β-estradiol, progesterone, DHEA and testosterone. The differences in hormone levels we noted between mycetoma patients and healthy controls did not directly affect the fungus itself. Indirect effects on the patients' hormone regulated immune states are the more likely explanations for mycetoma susceptibility.

  2. Crystal structure of a raw-starch-degrading bacterial α-amylase belonging to subfamily 37 of the glycoside hydrolase family GH13

    Science.gov (United States)

    Liu, Yanhong; Yu, Jigang; Li, Fudong; Peng, Hui; Zhang, Xuecheng; Xiao, Yazhong; He, Chao

    2017-01-01

    Subfamily 37 of the glycoside hydrolase family GH13 was recently established on the basis of the discovery of a novel α-amylase, designated AmyP, from a marine metagenomic library. AmyP exhibits raw-starch-degrading activity and consists of an N-terminal catalytic domain and a C-terminal starch-binding domain. To understand this newest subfamily, we determined the crystal structure of the catalytic domain of AmyP, named AmyPΔSBD, complexed with maltose, and the crystal structure of the E221Q mutant AmyPΔSBD complexed with maltotriose. Glu221 is one of the three conserved catalytic residues, and AmyP is inactivated by the E221Q mutation. Domain B of AmyPΔSBD forms a loop that protrudes from domain A, stabilizes the conformation of the active site and increases the thermostability of the enzyme. A new calcium ion is situated adjacent to the -3 subsite binding loop and may be responsible for the increased thermostability of the enzyme after the addition of calcium. Moreover, Tyr36 participates in both stacking and hydrogen bonding interactions with the sugar motif at subsite -3. This work provides the first insights into the structure of α-amylases belonging to subfamily 37 of GH13 and may contribute to the rational design of α-amylase mutants with enhanced performance in biotechnological applications. PMID:28303907

  3. Dock6, a Dock-C subfamily guanine nucleotide exchanger, has the dual specificity for Rac1 and Cdc42 and regulates neurite outgrowth.

    Science.gov (United States)

    Miyamoto, Yuki; Yamauchi, Junji; Sanbe, Atsushi; Tanoue, Akito

    2007-02-15

    Small GTPases of the Rho family, Rho, Rac, and Cdc42, are critical regulators of the changes in the actin cytoskeleton. Rho GTPases are typically activated by Dbl-homology (DH)-domain-containing guanine nucleotide exchange factors (GEFs). Recent genetic and biochemical studies revealed a new type of GEF for the Rho GTPases. This family is composed of 11 genes, designated as Dock1 to Dock11, and is structurally divided into four classes Dock-A, -B, -C, and -D. Dock-A and -B subfamilies are typically GEFs specific for Rac1, while the Dock-D subfamily is specific for Cdc42. Here we show that Dock6, a member of the Dock-C subfamily, exchanges GDP for GTP for Rac1 and Cdc42 in vitro and in vivo. Furthermore, we find that, in mouse N1E-115 neuroblastoma cells, expression of Dock6 is increased following differentiation. Transfection of the catalytic Dock Homology Region-2 (DHR-2) domain of Dock6 promotes neurite outgrowth mediated by Rac1 and Cdc42. Conversely, knockdown of endogenous Dock6 by small interference RNA reduces activation of Rac1 and Cdc42 and neurite outgrowth. Taken together, these results suggest that Dock6 differs from all of the identified Dock180-related proteins, in that it is the GEF specific for both Rac1 and Cdc42 and may be one of physiological regulators of neurite outgrowth.

  4. Littorally adaptive? Testing the link between habitat, morphology, and reproduction in the intertidal sculpin subfamily Oligocottinae (Pisces: Cottoidea)

    Science.gov (United States)

    Burns, Michael D.; López, J. Andrés

    2017-01-01

    While intertidal habitats are often productive, species-rich environments, they are also harsh and highly dynamic. Organisms that live in these habitats must possess morphological and physiological adaptations that enable them to do so. Intertidal fishes are generally small, often lack scales, and the diverse families represented in intertidal habitats often show convergence into a few general body shapes. However, few studies have quantified the relationship between phenotypes and intertidal living. Likewise, the diversity of reproductive traits and parental care in intertidal fishes has yet to be compared quantitatively with habitat. We examine the relationship of these characters in the sculpin subfamily Oligocottinae using a phylogenetic hypothesis, geometric morphometrics, and phylogenetic comparative methods to provide the first formal test of associations between fish phenotypes and reproductive characters with intertidal habitats. We show that the ability to live in intertidal habitats, particularly in tide pools, is likely a primitive state for Oligocottinae, with a single species that has secondarily come to occupy only subtidal habitats. Contrary to previous hypotheses, maximum size and presence of scales do not show a statistically significant correlation with depth. However, the maximum size for all species is generally small (250 mm or less) and all show a reduction in scales, as would be expected for an intertidal group. Also contrary to previous hypotheses, we show that copulation and associated characters are the ancestral condition in Oligocottinae, with copulation most likely being lost in a single lineage within the genus Artedius. Lastly, we show that body shape appears to be constrained among species with broader depth ranges, but lineages that occupy only a narrow range of intertidal habitats display novel body shapes, and this may be associated with habitat partitioning, particularly as it relates to the degree of wave exposure. PMID

  5. Littorally adaptive? Testing the link between habitat, morphology, and reproduction in the intertidal sculpin subfamily Oligocottinae (Pisces: Cottoidea

    Directory of Open Access Journals (Sweden)

    Thaddaeus J. Buser

    2017-08-01

    Full Text Available While intertidal habitats are often productive, species-rich environments, they are also harsh and highly dynamic. Organisms that live in these habitats must possess morphological and physiological adaptations that enable them to do so. Intertidal fishes are generally small, often lack scales, and the diverse families represented in intertidal habitats often show convergence into a few general body shapes. However, few studies have quantified the relationship between phenotypes and intertidal living. Likewise, the diversity of reproductive traits and parental care in intertidal fishes has yet to be compared quantitatively with habitat. We examine the relationship of these characters in the sculpin subfamily Oligocottinae using a phylogenetic hypothesis, geometric morphometrics, and phylogenetic comparative methods to provide the first formal test of associations between fish phenotypes and reproductive characters with intertidal habitats. We show that the ability to live in intertidal habitats, particularly in tide pools, is likely a primitive state for Oligocottinae, with a single species that has secondarily come to occupy only subtidal habitats. Contrary to previous hypotheses, maximum size and presence of scales do not show a statistically significant correlation with depth. However, the maximum size for all species is generally small (250 mm or less and all show a reduction in scales, as would be expected for an intertidal group. Also contrary to previous hypotheses, we show that copulation and associated characters are the ancestral condition in Oligocottinae, with copulation most likely being lost in a single lineage within the genus Artedius. Lastly, we show that body shape appears to be constrained among species with broader depth ranges, but lineages that occupy only a narrow range of intertidal habitats display novel body shapes, and this may be associated with habitat partitioning, particularly as it relates to the degree of wave

  6. Morphological "primary homology" and expression of AG-subfamily MADS-box genes in pines, podocarps, and yews.

    Science.gov (United States)

    Englund, Marie; Carlsbecker, Annelie; Engström, Peter; Vergara-Silva, Francisco

    2011-01-01

    The morphological variation among reproductive organs of extant gymnosperms is remarkable, especially among conifers. Several hypotheses concerning morphological homology between various conifer reproductive organs have been put forward, in particular in relation to the pine ovuliferous scale. Here, we use the expression patterns of orthologs of the ABC-model MADS-box gene AGAMOUS (AG) for testing morphological homology hypotheses related to organs of the conifer female cone. To this end, we first developed a tailored 3'RACE procedure that allows reliable amplification of partial sequences highly similar to gymnosperm-derived members of the AG-subfamily of MADS-box genes. Expression patterns of two novel conifer AG orthologs cloned with this procedure-namely PodAG and TgAG, obtained from the podocarp Podocarpus reichei and the yew Taxus globosa, respectively-are then further characterized in the morphologically divergent female cones of these species. The expression patterns of PodAG and TgAG are compared with those of DAL2, a previously discovered Picea abies (Pinaceae) AG ortholog. By treating the expression patterns of DAL2, PodAG, and TgAG as character states mapped onto currently accepted cladogram topologies, we suggest that the epimatium-that is, the podocarp female cone organ previously postulated as a "modified" ovuliferous scale-and the canonical Pinaceae ovuliferous scale can be legitimally conceptualized as "primary homologs." Character state mapping for TgAG suggests in turn that the aril of Taxaceae should be considered as a different type of organ. This work demonstrates how the interaction between developmental-genetic data and formal cladistic theory could fruitfully contribute to gymnosperm systematics.

  7. A revised phylogenetic classification of the ant subfamily Formicinae (Hymenoptera: Formicidae), with resurrection of the genera Colobopsis and Dinomyrmex.

    Science.gov (United States)

    Ward, Philip S; Blaimer, Bonnie B; Fisher, Brian L

    2016-02-02

    The classification of the ant subfamily Formicinae is revised to reflect findings from a recent molecular phylogenetic study and complementary morphological investigations. The existing classification is maintained as far as possible, but some tribes and genera are redefined to ensure monophyly. Eleven tribes are recognized, all of which are strongly supported as monophyletic groups: Camponotini, Formicini, Gesomyrmecini, Gigantiopini, Lasiini (= Prenolepidii syn. n.), Melophorini (= Myrmecorhynchini syn. n.; = Notostigmatini syn. n.), Myrmelachistini stat. rev. (= Brachymyrmicini syn. n.), Myrmoteratini, Oecophyllini, Plagiolepidini, and Santschiellini stat. rev. Most of the tribes remain similar in content, but the generic composition of Lasiini, Melophorini, and Plagiolepidini is changed substantially. Species that have been placed in the genus Camponotus belong to three separate lineages. To ensure monophyly of this large, cosmopolitan genus we institute the following changes: Colobopsis and Dinomyrmex, both former subgenera of Camponotus, are elevated to genus level (stat. rev.), and two former genera, Forelophilus and Phasmomyrmex, are demoted to subgenus status (stat. n. and stat. rev., respectively) under Camponotus; two erstwhile subgenera of Phasmomyrmex, Myrmorhachis and Myrmacantha, become junior synonyms (syn. n.) of Camponotus (Phasmomyrmex); and the Camponotus subgenus Myrmogonia becomes a junior synonym (syn. n.) of Colobopsis. Dinomyrmex, represented by a single species from southeast Asia, D. gigas, is quite distinctive, but Camponotus and Colobopsis exhibit more subtle differences, despite being well separated phylogenetically. We identify morphological features of the worker caste that are broadly useful for distinguishing these two genera. Colobopsis species on the islands of New Caledonia and Fiji-regions with few native Camponotus species-tend to exceed these diagnostic bounds, but in this case regionally applicable character differences can

  8. Stereochemistry of Fuscumol and Fuscumol Acetate Influences Attraction of Longhorned Beetles (Coleoptera: Cerambycidae) of the Subfamily Lamiinae.

    Science.gov (United States)

    Hughes, G P; Meier, L R; Zou, Y; Millar, J G; Hanks, L M; Ginzel, M D

    2016-10-01

    The chemical structures of aggregation-sex pheromones of longhorned beetles (Coleoptera: Cerambycidae) are often conserved among closely related taxa. In the subfamily Lamiinae, adult males and females of several species are attracted by racemic blends of (E)-6,10-dimethyl-5,9-undecadien-2-ol (termed fuscumol) and the structurally related (E)-6,10-dimethyl-5,9-undecadien-2-yl acetate (fuscumol acetate). Both compounds have a chiral center, so each can exist in two enantiomeric forms. Males of many species of longhorned beetles only produce one stereoisomer of each pheromone component, and attraction may be reduced by the presence of stereoisomers that are not produced by a particular species. In a previous publication, analysis of headspace volatiles of adult beetles of the lamiine species Astyleiopus variegatus (Haldeman) revealed that males sex-specifically produced (S)-fuscumol and (S)-fuscumol acetate. Here, we describe field trials which tested attraction of this species to single enantiomers of fuscumol and fuscumol acetate, or to blends of enantiomers. We confirmed attraction of A. variegatus to its species-specific blend, but during the course of the trials, found that several other species also were attracted. These included Aegomorphus modestus (Gyllenhall), attracted to (S)-fuscumol acetate; Astylidius parvus (LeConte), attracted to (R)-fuscumol; Astylopsis macula (Say), attracted to (S)-fuscumol; and Graphisurus fasciatus (DeGeer), attracted to a blend of (R)-fuscumol and (R)-fuscumol acetate. These results suggest that chirality may be important in the pheromone chemistry of lamiines, and that specific stereoisomers or mixtures of stereoisomers are likely produced by each species.

  9. A novel fractal approach for predicting G-protein-coupled receptors and their subfamilies with support vector machines.

    Science.gov (United States)

    Nie, Guoping; Li, Yong; Wang, Feichi; Wang, Siwen; Hu, Xuehai

    2015-01-01

    G-protein-coupled receptors (GPCRs) are seven membrane-spanning proteins and regulate many important physiological processes, such as vision, neurotransmission, immune response and so on. GPCRs-related pathways are the targets of a large number of marketed drugs. Therefore, the design of a reliable computational model for predicting GPCRs from amino acid sequence has long been a significant biomedical problem. Chaos game representation (CGR) reveals the fractal patterns hidden in protein sequences, and then fractal dimension (FD) is an important feature of these highly irregular geometries with concise mathematical expression. Here, in order to extract important features from GPCR protein sequences, CGR algorithm, fractal dimension and amino acid composition (AAC) are employed to formulate the numerical features of protein samples. Four groups of features are considered, and each group is evaluated by support vector machine (SVM) and 10-fold cross-validation test. To test the performance of the present method, a new non-redundant dataset was built based on latest GPCRDB database. Comparing the results of numerical experiments, the group of combined features with AAC and FD gets the best result, the accuracy is 99.22% and Matthew's correlation coefficient (MCC) is 0.9845 for identifying GPCRs from non-GPCRs. Moreover, if it is classified as a GPCR, it will be further put into the second level, which will classify a GPCR into one of the five main subfamilies. At this level, the group of combined features with AAC and FD also gets best accuracy 85.73%. Finally, the proposed predictor is also compared with existing methods and shows better performances.

  10. Convergent, parallel and correlated evolution of trophic morphologies in the subfamily schizothoracinae from the Qinghai-Tibetan plateau.

    Science.gov (United States)

    Qi, Delin; Chao, Yan; Guo, Songchang; Zhao, Lanying; Li, Taiping; Wei, Fulei; Zhao, Xinquan

    2012-01-01

    Schizothoracine fishes distributed in the water system of the Qinghai-Tibetan plateau (QTP) and adjacent areas are characterized by being highly adaptive to the cold and hypoxic environment of the plateau, as well as by a high degree of diversity in trophic morphology due to resource polymorphisms. Although convergent and parallel evolution are prevalent in the organisms of the QTP, it remains unknown whether similar evolutionary patterns have occurred in the schizothoracine fishes. Here, we constructed for the first time a tentative molecular phylogeny of the schizothoracine fishes based on the complete sequences of the cytochrome b gene. We employed this molecular phylogenetic framework to examine the evolution of trophic morphologies. We used Pagel's maximum likelihood method to estimate the evolutionary associations of trophic morphologies and food resource use. Our results showed that the molecular and published morphological phylogenies of Schizothoracinae are partially incongruent with respect to some intergeneric relationships. The phylogenetic results revealed that four character states of five trophic morphologies and of food resource use evolved at least twice during the diversification of the subfamily. State transitions are the result of evolutionary patterns including either convergence or parallelism or both. Furthermore, our analyses indicate that some characters of trophic morphologies in the Schizothoracinae have undergone correlated evolution, which are somewhat correlated with different food resource uses. Collectively, our results reveal new examples of convergent and parallel evolution in the organisms of the QTP. The adaptation to different trophic niches through the modification of trophic morphologies and feeding behaviour as found in the schizothoracine fishes may account for the formation and maintenance of the high degree of diversity and radiations in fish communities endemic to QTP.

  11. The ZNF75 zinc finger gene subfamily: Isolation and mapping of the four members in humans and great apes

    Energy Technology Data Exchange (ETDEWEB)

    Villa, A.; Strina, D.; Frattini, A. [Consiglio Nazionale delle Ricerche, Milan (Italy)] [and others

    1996-07-15

    We have previously reported the characterization of the human ZNF75 gene located on Xq26, which has only limited homology (less than 65%) to other ZF genes in the databases. Here, we describe three human zinc finger genes with 86 to 95% homology to ZNF75 at the nucleotide level, which represent all the members of the human ZNF75 subfamily. One of these, ZNF75B, is a pseudogene mapped to chromosome 12q13. The other two, ZNF75A and ZNF75C, maintain on ORF in the sequenced region, and at least the latter is expressed in the U937 cell line. They were mapped to chromosomes 16 and 11, respectively. All these genes are conserved in chimpanzees, gorillas, and orangutans. The ZNF75B homologue is a pseudogene in all three great apes, and in chimpanzee it is located on chromosome 10 (phylogenetic XII), at p13 (corresponding to the human 12q13). The chimpanzee homologue of ZNF75 is also located on the Xq26 chromosome, in the same region, as detected by in situ hybridization. As expected, nucleotide changes were clearly more abundant between human and organutan than between human and chimpanzee or gorilla homologues. Members of the same class were more similar to each other than to the other homologues within the same species. This suggests that the duplication and/or retrotranscription events occurred in a common ancestor long before great ape speciation. This, together with the existance of at least two genes in cows and horses, suggests a relatively high conservation of this gene family. 20 refs., 5 figs., 1 tab.

  12. APL患者外周血TCR V α亚家族T细胞分布和增殖特点%Distribution and clonality of peripheral blood TCR Vαsubfamily T cells in patients with acute promyelocytic leukemia

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Objective: To investigate the distribution and clonality of TCR Vc subfamily T cells in patients with acute promyelocytic leukemia (APL). Methods: The complementary determining region 3 (CDR3) of TCR Vα 29 subfamily genes in peripheral blood mononuclear cells from 9 APL patients were amplified using RT-PCR. The positive products were further analyzed to identify the clonality of T cells by GeneScan technique. Results: One to seven of TCR Vα subfamilies could be detected in peripheral blood T cells from 9 cases with APL, the frequent expression of Vα subfamilies predominated in Vα3and Vα19. Clonal expanded T cells could be detected in 8 APL patients, which predominant used Vα3, Vα26 or Vα27 (3 out of 8 cases). However, almost all Vα subfamilies with polyclonal expansion could be detected in peripheral blood T cells from 10 cases of normal individuals. Conclusion: Remarkable skew distribution and clonal expansion of TCR Vα subfamilies T cells is the common feature in patients with APL. Clonal expansion of T cells might reflect a response in host to APL cell associated antigen, whether these expanded T cells have the ability for specific cytotoxicity against APL cells, remains an open question.

  13. Identification and characterization of three TLR1 subfamily members from the orange-spotted grouper, Epinephelus coioides.

    Science.gov (United States)

    Li, Yan-Wei; Xu, Dong-Dong; Li, Xia; Mo, Ze-Quan; Luo, Xiao-Chun; Li, An-Xing; Dan, Xue-Ming

    2016-08-01

    Toll-like receptors (TLRs), which play important roles in host defense against pathogen infection, are the most intensively studied pattern recognition receptors (PRRs). In this study, we identified three novel TLR1 subfamily members, including TLR1 (EcTLR1b), TLR2 (EcTLR2b) and TLR14 (EcTLR14), from the orange-spotted grouper (Epinephelus coioides). EcTLR1b and EcTLR2b displayed low sequence identity with the previously reported grouper TLR1 (EcTLR1a) and TLR2 (EcTLR2a), respectively. The open reading frames (ORFs) of EcTLR1b, EcTLR2b and EcTLR14 contain 2484 bp, 2394 bp and 2640 bp, which encode the corresponding 827 amino acids (aa), 797 aa and 879 aa, respectively. All three TLRs have leucine-rich repeat (LRR) domains (including an LRR-NT (except for EcTLR1b), several LRR motifs and an LRR-CT), a trans-membrane region and a Toll/interleukin-1 receptor (TIR) domain. The TIR domains of the three TLRs exhibited conserved boxes, namely box1, box2 and box3, and their 3D models were similar to those of human TLR1 or TLR2. Sequence alignment demonstrated that the TIR domains of the three TLRs shared higher sequence identity with those of other species than the full-length receptors. Phylogenetic analysis indicated that EcTLR1s and EcTLR2s are characterized by their differing evolutionary status, whereas EcTLR14 was found to be in the same group as other piscine TLR14/18s. The three TLRs were ubiquitously expressed in seven tested tissues of healthy groupers, although their expression profiles were different. Post Cryptocaryon irritans infection, TLR1s expression was up-regulated in the gills. The expression of TLR2b was mainly increased in the spleen, but decreased in the gills, which was similar to the expression pattern of TLR2a post C. irritans infection. Unlike EcTLR1b and EcTLR2b, however, the grouper TLR14 transcript was substantially induced in both tissues post challenge. These findings may be helpful in understanding the innate immune mechanism of host

  14. Evolution of a novel subfamily of nuclear receptors with members that each contain two DNA binding domains

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    Hirai Hirohisa

    2007-02-01

    Full Text Available Abstract Background Nuclear receptors (NRs are important transcriptional modulators in metazoans which regulate transcription through binding to the promoter region of their target gene by the DNA binding domain (DBD and activation or repression of mRNA synthesis through co-regulators bound to the ligand binding domain (LBD. NRs typically have a single DBD with a LBD. Results Three nuclear receptors named 2DBD-NRs, were identified from the flatworm Schistosoma mansoni that each possess a novel set of two DBDs in tandem with a LBD. They represent a novel NR modular structure: A/B-DBD-DBD-hinge-LBD. The 2DBD-NRs form a new subfamily of NRs, VII. By database mining, 2DBD-NR genes from other flatworm species (Schmidtea mediterranea and Dugesia japonica, from Mollusks (Lottia gigantean and from arthropods (Daphnia pulex were also identified. All 2DBD-NRs possess a P-box sequence of CEACKK in the first DBD, which is unique to 2DBD-NRs, and a P-box sequence of CEGCKG in the second DBD. Phylogenetic analyses of both DBD and ligand binding domain sequences showed that 2DBD-NR genes originate from a common two DBD-containing ancestor gene. A single 2DBD-NR orthologue was found in Arthropoda, Platyhelminths and Mollusca. Subsequent 2DBD-NR gene evolution in Mollusks and Platyhelminths involved gene duplication. Chromosome localization of S. mansoni 2DBD-NR genes by Fluorescent in situ hybridization (FISH suggests that 2DBD-NR genes duplicated on different chromosomes in the Platyhelminths. Dimerization of Sm2DBDα indicates that 2DBD-NRs may act as homodimers, suggesting either that two repeats of a half-site are necessary for each DBD of 2DBD-NRs to bind to its target gene, or that each 2DBD-NR can recognize multiple sites. Conclusion 2DBD-NRs share a common ancestor gene which possessed an extra DBD that likely resulted from a recombination event. After the split of the Arthropods, Mollusks and Platyhelminths, 2DBD-NR underwent a recent duplication in a

  15. Phylogenetic relationships and biogeographical patterns in Circum-Mediterranean subfamily Leuciscinae (Teleostei, Cyprinidae inferred from both mitochondrial and nuclear data

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    Perea Silvia

    2010-08-01

    Full Text Available Abstract Background Leuciscinae is a subfamily belonging to the Cyprinidae fish family that is widely distributed in Circum-Mediterranean region. Many efforts have been carried out to deciphering the evolutionary history of this group. Thus, different biogeographical scenarios have tried to explain the colonization of Europe and Mediterranean area by cyprinids, such as the "north dispersal" or the "Lago Mare dispersal" models. Most recently, Pleistocene glaciations influenced the distribution of leuciscins, especially in North and Central Europe. Weighing up these biogeographical scenarios, this paper constitutes not only the first attempt at deciphering the mitochondrial and nuclear relationships of Mediterranean leuciscins but also a test of biogeographical hypotheses that could have determined the current distribution of Circum-Mediterranean leuciscins. Results A total of 4439 characters (mitochondrial + nuclear from 321 individuals of 176 leuciscine species rendered a well-supported phylogeny, showing fourteen main lineages. Analyses of independent mitochondrial and nuclear markers supported the same main lineages, but basal relationships were not concordant. Moreover, some incongruence was found among independent mitochondrial and nuclear phylogenies. The monophyly of some poorly known genera such as Pseudophoxinus and Petroleuciscus was rejected. Representatives of both genera belong to different evolutionary lineages. Timing of cladogenetic events among the main leuciscine lineages was gained using mitochondrial and all genes data set. Conclusions Adaptations to a predatory lifestyle or miniaturization have superimposed the morphology of some species. These species have been separated into different genera, which are not supported by a phylogenetic framework. Such is the case of the genera Pseudophoxinus and Petroleuciscus, which real taxonomy is not well known. The diversification of leuciscine lineages has been determined by intense

  16. First record of the subfamily Proctolabinae (Orthoptera: Acridoidea: Acrididae from Argentina Primer registro de la subfamilia Proctolabinae (Orthoptera: Acridoidea: Acrididae para la Argentina

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    Christian Bardi

    2010-12-01

    Full Text Available This contribution records for the first time the subfamily Proctolabinae from Argentina. This subfamily contains 29 genera and 209 species restricted to the Neotropics with only one genus, Eucephalacris Descamps, reaching south as far as Mato Grosso in Brazil and northern Paraguay. Specimens belonging to Eucephalacris borellii (Giglio-Tos were collected in Misiones province. The presence of this species registered herein raises to eleven the number of Acrididae subfamilies known to occur in the country, and highlights the importance of conducting surveys of Acridoidea and Orthoptera in general, in diverse regions of Argentina. Brief diagnoses and illustrations of the characters that allowed the identification of the genus and species are also given in this contribution.Esta contribución registra por primera vez la subfamilia Proctolabinae para la Argentina. La subfamilia Proctolabinae contiene 29 géneros y 209 especies restringidas a la región Neotropical, con sólo uno de sus géneros, Eucephalacris Descamps, que llega al sur hasta Mato Grosso en Brasil y el norte de Paraguay. Ejemplares pertenecientes a Eucephalacris borellii (Giglio-Tos fueron colectados en el departamento de Guaraní, provincia de Misiones. La presencia de Eucephalacris borellii, registrada en este trabajo, eleva a once el número de subfamilias de Acrididae presentes en la Argentina, y destaca la necesidad de realizar relevamientos sobre la diversidad de Acridoidea y de Orthoptera en general, en diversas regiones de nuestro país. También se brindan en esta contribución una breve diagnosis e ilustraciones de los caracteres que permiten la identificación del género y de la especie.

  17. Functional

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    Fedoua Gandia

    2014-07-01

    Full Text Available The study was carried out to investigate the effects of inhaled Mg alone and associated with F in the treatment of bronchial hyperresponsiveness. 43 male Wistar rats were randomly divided into four groups and exposed to inhaled NaCl 0.9%, MeCh, MgSO4 and MgF2. Pulmonary changes were assessed by means of functional tests and quantitative histological examination of lungs and trachea. Results revealed that delivery of inhaled Mg associated with F led to a significant decrease of total lung resistance better than inhaled Mg alone (p < 0.05. Histological examinations illustrated that inhaled Mg associated with F markedly suppressed muscular hypertrophy (p = 0.034 and bronchoconstriction (p = 0.006 in MeCh treated rats better than inhaled Mg alone. No histological changes were found in the trachea. This study showed that inhaled Mg associated with F attenuated the main principle of the central components of changes in MeCh provoked experimental asthma better than inhaled Mg alone, potentially providing a new therapeutic approach against asthma.

  18. Biting midges of the subfamily Forcipomyiinae (Diptera: Ceratopogonidae) from the Middle East, with keys and descriptions of new species.

    Science.gov (United States)

    Alwin-Kownacka, Alicja; Szadziewski, Ryszard; Szwedo, Jacek

    2016-10-05

    Middle East biting midges of the genera Atrichopogon Kieffer and Forcipomyia Meigen, subfamily Forcipomyiinae Lenz, covering 41 species are reviewed. Two new species are described and illustrated: Forcipomyia (F.) siverekensis Alwin & Szadziewski sp. nov. and Forcipomyia (Microhelea) borkenti Alwin & Szadziewski sp. nov. The list includes 16 species of Atrichopogon and 25 of Forcipomyia. Nine species previously described by Vimmer and Kieffer from the Middle East are treated as nomina dubia and not included in the list.        Keys to identification of Atrichopogon and Forcipomyia species of the Middle East are also provided.

  19. A review of the mite subfamily Harpirhynchinae (Acariformes: Harpirhynchidae)--parasites of New World birds (Aves: Neognathae).

    Science.gov (United States)

    Bochkov, Andre V; OConnor, Barry M; Klompen, Hans

    2015-09-30

    Mites of the subfamily Harpirhynchinae (Acariformes: Cheyletoidea: Harpirhynchidae) associated with neognathous birds (Aves: Neognathae) in the New World are revised. In all, 68 species in 8 genera are recorded. Among them, 27 new species and 1 new genus are described as new for science: Harpyrhynchoides gallowayi Bochkov, OConnor and Klompen sp. nov. from Columba livia (Columbiformes: Columbidae) from Canada (Manitoba), H. zenaida Bochkov, OConnor and Klompen sp. nov. from Zenaida macroura (Columbiformes: Columbidae) from USA (Michigan), H. calidris Bochkov, OConnor and Klompen sp. nov. from Calidris minutilla (Charadriiformes: Scolopacidae) from USA (Kansas), H. actitis Bochkov, OConnor and Klompen sp. nov. from Actitis macularius (Charadriiformes: Scolopacidae) from Canada (British Columbia), H. charadrius Bochkov, OConnor and Klompen sp. nov. from Charadrius vociferus (Charadriiformes: Charadriidae) from USA (Texas), H. pluvialis Bochkov, OConnor and Klompen sp. nov. from Pluvialis dominica (Charadriiformes: Charadriidae) from USA (Ohio), H. bubulcus Bochkov, OConnor and Klompen sp. nov. from Bubulcus ibis (Pelecaniformes: Ardeidae) from USA (Florida), H. ixobrychus Bochkov, OConnor and Klompen sp. nov. from Ixobrychus exilis (Pelecaniformes: Ardeidae) from USA (Michigan), H. puffinus Mertins sp. nov. from Puffinus gravis (Procellariformes: Procellariidae) from USA (Florida), H. megascops Bochkov, OConnor and Klompen sp. nov. from Megascops asio (Strigiformes: Strigidae) from USA (Michigan), H. athene Bochkov, OConnor and Klompen sp. nov. from Athene canicularia (Strigiformes: Strigidae) from USA (Texas), H. coccyzus Bochkov, OConnor and Klompen sp. nov. from Coccyzus americanus (Cuculiformes: Cuculidae) from USA (Michigan), H. crotophaga Bochkov, OConnor and Klompen sp. nov. from Crotophaga ani (Cuculiformes: Cuculidae) from Suriname; Crassacarus Bochkov, OConnor and Klompen, gen. nov.: Crassacarus alexfaini Bochkov, OConnor and Klompen sp. nov. (type of genus

  20. A putative autonomous 20.5 kb-CACTA transposon insertion in an F3'H allele identifies a new CACTA transposon subfamily in Glycine max

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    Vodkin Lila

    2008-12-01

    in the gray trichome allele t*. Conclusion The molecular characterization of a 20.5 kb insertion in the flavonoid 3'-hydroxylase (F3'H gene of a soybean gray pubescence allele (t* identified the structure of a CACTA transposon designated Tgmt*. Besides the terminal inverted repeats and subterminal repeated motifs,Tgmt* encoded a large gene with two putative functions that are required for excision and transposition of a CACTA element, a transposase and the DNA binding protein known to associate to the subterminal repeated motifs. The degree of dissimilarity between Tgmt* transposase and subterminal repeated motifs with those of previously characterized defective CACTA elements (Tgm1-7 were evidence of the existence of two subfamilies of CACTA transposons in soybean, an observation not previously reported in other plants. In addition, our analyses of a genetically active and potentially autonomous element sheds light on the complete structure of a soybean element that is useful for annotation of the repetitive fraction of the soybean genome sequence and may prove useful for transposon tagging or transposon display experiments in different genetic lines.

  1. Genome-wide identification of nuclear receptor (NR) genes and the evolutionary significance of the NR1O subfamily in the monogonont rotifer Brachionus spp.

    Science.gov (United States)

    Kim, Duck-Hyun; Kim, Hui-Su; Hwang, Dae-Sik; Kim, Hee-Jin; Hagiwara, Atsushi; Lee, Jae-Seong; Jeong, Chang-Bum

    2017-10-01

    Nuclear receptors (NRs) are a large family of transcription factors that are involved in many fundamental biological processes. NRs are considered to have originated from a common ancestor, and are highly conserved throughout the whole animal taxa. Therefore, the genome-wide identification of NR genes in an animal taxon can provide insight into the evolutionary tendencies of NRs. Here, we identified all the NR genes in the monogonont rotifer Brachionus spp., which are considered an ecologically key species due to their abundance and world-wide distribution. The NR family was composed of 40, 32, 29, and 32 genes in the genomes of the rotifers B. calyciflorus, B. koreanus, B. plicatilis, and B. rotundiformis, respectively, which were classified into seven distinct subfamilies. The composition of each subfamily was highly conserved between species, except for NR1O genes, suggesting that they have undergone sporadic evolutionary processes for adaptation to their different environmental pressures. In addition, despite the dynamics of NR evolution, the significance of the conserved endocrine system, particularly for estrogen receptor (ER)-signaling, in rotifers was discussed on the basis of phylogenetic analyses. The results of this study may help provide a better understanding the evolution of NRs, and expand our knowledge of rotifer endocrine systems. Copyright © 2017 Elsevier Inc. All rights reserved.

  2. A subfamily of putative cytokinin receptors is revealed by an analysis of the evolution of the two-component signaling system of plants.

    Science.gov (United States)

    Gruhn, Nijuscha; Halawa, Mhyeddeen; Snel, Berend; Seidl, Michael F; Heyl, Alexander

    2014-05-01

    The two-component signaling system--the major signaling pathway of bacteria--is found among higher eukaryotes only in plants, where it regulates diverse processes, such as the signaling of the phytohormone cytokinin. Cytokinin is perceived by a hybrid histidine (His) kinase receptor, and the signal is transduced by a multistep phosphorelay system of His phosphotransfer proteins and different classes of response regulators (RRs). To shed light on the origin and evolution of the two-component signaling system members in plants, we conducted a comprehensive domain-based phylogenetic study across the relevant kingdoms, including Charophyceae algae, the group of green algae giving rise to land plants. Surprisingly, we identified a subfamily of cytokinin receptors with members only from the early diverging land plants Marchantia polymorpha and Physcomitrella patens and then experimentally characterized two members of this subfamily. His phosphotransfer proteins of Charophyceae seemed to be more closely related to land plants than to other groups of green algae. Farther down the signaling pathway, the type-B RRs were found across all plant clades, but many members lack either the canonical Asp residue or the DNA binding domain. In contrast, the type-A RRs seemed to be limited to land plants. Finally, the analysis provided hints that one additional group of RRs, the type-C RRs, might be degenerated receptors and thus, of a different evolutionary origin than bona fide RRs.

  3. 水蛇亚科形态学特征的支序分析%Morphological Phylogeny of the Water Snake Subfamily Homalopsinae (Serpent: Colubridae)

    Institute of Scientific and Technical Information of China (English)

    吕顺清; 庞峻锋; 杨大同

    2006-01-01

    The morphological phylogeny of the water snake subfamily Homalopsinae, containing 10 genera, of which seven are monotypic, was not reported up until now. Here fourteen morphological characters were selected for the cladistic analysis. Using software Hennig 86, two phylogenetic trees were inferred and the results showed that the subfamily Homalopsinae was divided into two groups. Compared with the molecular phylonenetic tree of Voris et al (2002), the genera Gerarda and Fordonia are sister groups in both studies; both studies also yielded the same monophyletic lineage, which contained three genera ( Cerberus + Erpeton + Homalopsis ). However, the position of the genus Cantoria is distinctly different with the study of Voris et al(2002).%水蛇亚科属于游蛇科,包含10个属.其中7个属为单型属.选取水蛇亚科14个形态学特征进行支序分析,并利用计算机软件Hennig 86对水蛇亚科中8个属之间的系统发育关系进行初步探讨,结果显示水蛇亚科分为两支:Gerarda和Fordonia两个属构成姊妹群,Cerberus、Erpeton和Homalopsis三个属也构成单系群,与Voris et al(2002)的分子系统树相同,但Cantoria属的地位则与Voris et al(2002)的明显不同.

  4. Key to larvae of the South American subfamilies of weevils (Coleoptera, Curculionoidea Clave para larvas de las subfamilias sudamericanas de gorgojos (Coleoptera, Curculionoidea

    Directory of Open Access Journals (Sweden)

    ADRIANA E. MARVALDI

    2003-12-01

    Full Text Available The weevils (Coleoptera: Curculionoidea from South America are classsified into seven families and 28 subfamilies as follows: Nemonychidae (Rhinorhynchinae, Anthribidae (Anthribinae, Belidae (Belinae and Oxycoryninae, Attelabidae (Attelabinae and Rhynchitinae, Brentidae (Apioninae and Brentinae, Caridae (Carinae and Curculionidae (Erirhininae, Dryophthorinae, Entiminae, Aterpinae, Gonipterinae, Rhythirrininae, Thecesterninae, Eugnominae, Hyperinae, Curculioninae, Cryptorhynchinae, Mesoptiliinae (= Magdalidinae, Molytinae, Baridinae, Lixinae, Conoderinae (= Zygopinae, Cossoninae, Scolytinae and Platypodinae. A dichotomous key for the larval stage is provided for identification of the families and subfamilies of Curculionoidea present in South America. The key is based on external morphological characters and contains data on larval feeding habitsLos gorgojos (Coleoptera: Curculionoidea de Sudamérica están clasificados en siete familias y 28 subfamilias como se muestra a continuación: Nemonychidae (Rhinorhynchinae, Anthribidae (Anthribinae, Belidae (Belinae y Oxycoryninae, Attelabidae (Attelabinae y Rhynchitinae, Brentidae (Apioninae y Brentinae, Caridae (Carinae y Curculionidae (Erirhininae, Dryophthorinae, Entiminae, Aterpinae, Gonipterinae, Rhythirrininae, Thecesterninae, Eugnominae, Hyperinae, Curculioninae, Cryptorhynchinae, Mesoptiliinae (= Magdalidinae, Molytinae, Baridinae, Lixinae, Conoderinae (= Zygopinae, Cossoninae, Scolytinae y Platypodinae. Se brinda una clave dicotómica para el estado de larva de Curculionoidea en Sudamérica, para su determinación a nivel de familias y subfamilias. La clave está basada sobre caracteres morfológicos externos y se presentan además datos de hábitos alimentarios

  5. Distinct structural and redox properties of the heme active site in bacterial dye decolorizing peroxidase-type peroxidases from two subfamilies: resonance Raman and electrochemical study.

    Science.gov (United States)

    Sezer, Murat; Santos, Ana; Kielb, Patrycja; Pinto, Tiago; Martins, Ligia O; Todorovic, Smilja

    2013-05-07

    Spectroscopic data of dye decolorizing peroxidases (DyPs) from Bacillus subtilis (BsDyP), an A subfamily member, and Pseudomonas putida (PpDyP), a B subfamily enzyme, reveal distinct heme coordination patterns of the respective active sites. In solution, both enzymes show a heterogeneous spin population, with the six-coordinated low-spin state being the most populated in the former and the five-coordinated quantum mechanically mixed-spin state in the latter. We ascribe the poor catalytic activity of BsDyP to the presence of a catalytically incompetent six-coordinated low-spin population. The spin populations of the two DyPs are sensitively dependent on the pH, temperature, and physical, i.e., solution versus crystal versus immobilized, state of the enzymes. We observe a redox potential for the Fe(2+)/Fe(3+) couple in BsDyP (-40 mV) at pH 7.6 substantially more positive than those reported for the majority of other peroxidases, including PpDyP (-260 mV). Furthermore, we evaluate the potential of the studied enzymes for biotechnological applications on the basis of electrochemical and spectroelectrochemical data.

  6. Crystal structure and biochemical investigations reveal novel mode of substrate selectivity and illuminate substrate inhibition and allostericity in a subfamily of Xaa-Pro dipeptidases.

    Science.gov (United States)

    Are, Venkat N; Kumar, Ashwani; Kumar, Saurabh; Goyal, Venuka Durani; Ghosh, Biplab; Bhatnagar, Deepak; Jamdar, Sahayog N; Makde, Ravindra D

    2017-02-01

    Xaa-Pro dipeptidase (XPD) catalyzes hydrolysis of iminopeptide bond in dipeptides containing trans-proline as a second residue. XPDs are found in all living organisms and are believed to play an essential role in proline metabolism. Here, we report crystal structures and extensive enzymatic studies of XPD from Xanthomonas campestris (XPDxc), the first such comprehensive study of a bacterial XPD. We also report enzymatic activities of its ortholog from Mycobacterium tuberculosis (XPDmt). These enzymes are strictly dipeptidases with broad substrate specificities. They exhibit substrate inhibition and allostericity, as described earlier for XPD from Lactococcus lactis (XPDll). The structural, mutational and comparative data have revealed a novel mechanism of dipeptide selectivity and substrate binding in these enzymes. Moreover, we have identified conserved sequence motifs that distinguish these enzymes from other prolidases, thus defining a new subfamily. This study provides a suitable structural template for explaining unique properties of this XPDxc subfamily. In addition, we report unique structural features of XPDxc protein like an extended N-terminal tail region and absence of a conserved Tyr residue near the active site.

  7. A phylogenetic analysis using multidirectional chromosome painting of three species (Uroderma magnirostrum, U. bilobatum and Artibeus obscurus) of subfamily Stenodermatinae (Chiroptera-Phyllostomidae).

    Science.gov (United States)

    Pieczarka, J C; Gomes, A J B; Nagamachi, C Y; Rocha, D C C; Rissino, J D; O'Brien, P C M; Yang, F; Ferguson-Smith, M A

    2013-07-01

    The species of genera Uroderma and Artibeus are medium-sized bats belonging to the family Phyllostomidae and subfamily Stenodermatinae (Mammalia, Chiroptera) from South America. They have a wide distribution in the Neotropical region, with two currently recognized species in Uroderma and approximately 20 species in Artibeus. These two genera have different rates of chromosome evolution, with Artibeus probably having retained the ancestral karyotype for the subfamily. We used whole chromosome paint probe sets from Carollia brevicauda and Phyllostomus hastatus on Uroderma magnirostrum, Uroderma bilobatum, and Artibeus obscurus. With the aim of testing the previous phylogenies of these bats using cytogenetics, we compared these results with published painting maps on Phyllostomidae. The genome-wide comparative maps based on chromosome painting and chromosome banding reveal the chromosome forms that characterize each taxonomic level within the Phyllostomidae and show the chromosome evolution of this family. Based on this, we are able to suggest an ancestral karyotype for Phyllostomidae. Our cladistic analysis is an independent confirmation using multidirectional chromosome painting of the previous Phyllostomidae phylogenies.

  8. iDPF-PseRAAAC: A Web-Server for Identifying the Defensin Peptide Family and Subfamily Using Pseudo Reduced Amino Acid Alphabet Composition.

    Directory of Open Access Journals (Sweden)

    Yongchun Zuo

    Full Text Available Defensins as one of the most abundant classes of antimicrobial peptides are an essential part of the innate immunity that has evolved in most living organisms from lower organisms to humans. To identify specific defensins as interesting antifungal leads, in this study, we constructed a more rigorous benchmark dataset and the iDPF-PseRAAAC server was developed to predict the defensin family and subfamily. Using reduced dipeptide compositions were used, the overall accuracy of proposed method increased to 95.10% for the defensin family, and 98.39% for the vertebrate subfamily, which is higher than the accuracy from other methods. The jackknife test shows that more than 4% improvement was obtained comparing with the previous method. A free online server was further established for the convenience of most experimental scientists at http://wlxy.imu.edu.cn/college/biostation/fuwu/iDPF-PseRAAAC/index.asp. A friendly guide is provided to describe how to use the web server. We anticipate that iDPF-PseRAAAC may become a useful high-throughput tool for both basic research and drug design.

  9. An experimentally validated panel of subfamily-specific oligonucleotide primers (V alpha 1-w29/V beta 1-w24) for the study of human T cell receptor variable V gene segment usage by polymerase chain reaction.

    Science.gov (United States)

    Genevée, C; Diu, A; Nierat, J; Caignard, A; Dietrich, P Y; Ferradini, L; Roman-Roman, S; Triebel, F; Hercend, T

    1992-05-01

    We report here the characterization of a series of T cell receptor (TcR) V alpha or V beta subfamily-specific oligonucleotide primers. Criteria that have guided the design of each oligonucleotide include appropriate thermodynamic parameters as well as differential base-pairing scores with related and unrelated target sequences. The specificity of the oligonucleotides for each V alpha or V beta subfamily was tested by polymerase chain reaction (PCR) on both a series of TcR encoding plasmid DNA and clonal T cell populations. Unexpected cross-reactivities were observed with plasmid cDNA sequences corresponding to unrelated subfamily gene segments. This led to the synthesis of additional series of oligonucleotides to obtain a relevant panel. A series of V alpha 1-w29/V beta 1-w24 TcR subfamily-specific oligonucleotides was eventually selected which generates little, if any, cross-reactivity. The use of C alpha or C beta primers for the amplification of internal positive control templates (i.e. C beta for the V alpha series and C alpha for the V beta series) has been tested in PCR performed with cDNA derived from peripheral blood lymphocytes; it was shown not to alter the amplification of the V subfamily-specific DNA fragments. This panel of oligonucleotides will be helpful in the study of TcRV gene segment usage and, thus, may lead to a better characterization of T cell responses in physiological and pathological situations.

  10. Dissecting molecular architecture of post-synaptic density at excitatory synapses: An Editorial Highlight for 'Hierarchical organization and genetically separable subfamilies of PSD95 postsynaptic supercomplexes' on page 504.

    Science.gov (United States)

    Chen, Jinjun; Pan, Hui-Lin

    2017-08-01

    This Editorial highlights a study by Frank and colleagues (2017) in the current issue of Journal of Neurochemistry. The authors report the genetic composition and stoichiometry of endogenous subfamilies of PSD95-containing supercomplexes in the mouse brain using an innovative strategy of combining gene-tagging knock-in, targeted mutations, and quantitative biochemical assays. Their findings shed new light on our understanding of the genetic hierarchy required for the assembly of distinct supercomplex subfamilies at excitatory synapses in the brain. © 2017 International Society for Neurochemistry.

  11. GPCRTree: online hierarchical classification of GPCR function

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    Timmis Jon

    2008-08-01

    Full Text Available Abstract Background G protein-coupled receptors (GPCRs play important physiological roles transducing extracellular signals into intracellular responses. Approximately 50% of all marketed drugs target a GPCR. There remains considerable interest in effectively predicting the function of a GPCR from its primary sequence. Findings Using techniques drawn from data mining and proteochemometrics, an alignment-free approach to GPCR classification has been devised. It uses a simple representation of a protein's physical properties. GPCRTree, a publicly-available internet server, implements an algorithm that classifies GPCRs at the class, sub-family and sub-subfamily level. Conclusion A selective top-down classifier was developed which assigns sequences within a GPCR hierarchy. Compared to other publicly available GPCR prediction servers, GPCRTree is considerably more accurate at every level of classification. The server has been available online since March 2008 at URL: http://igrid-ext.cryst.bbk.ac.uk/gpcrtree/.

  12. Typification of taxa of subfamily Silenoideae (Caryophyllaceae Juss. from Siberia and Russian Far East based on materials kept in the Herbarium of the Komarov Botanical Institute (LE

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    G. A. Lazkov

    2016-06-01

    Full Text Available Data on type material of previously not typified taxa of the subfamily Silenoideae (Caryophyllaceae Juss., kept in the Herbarium of the Komarov Botanical Institute (LE are summarized in the paper. All relevant taxa including eight species (or subsequently accepted as species: Gastrolychnis violascens Tolm., Gypsophila stricta Bunge, Heterochroa petraea Bunge, Lychnis ajanensis var. villosula Trautv. [L. villosula (Trautv. Gorschk.], L. fulgens var. wilfordi Regel [L. wilfordi (Regel Maxim.], L. tristis Bunge, Melandrium olgae Maxim., Silene melandriiformis Maxim., five varieties (Melandrium affine var. Intermedium Tolm., Silene repens var. pratensis Kom., S. repens var. alpina Kom., S. repens var. angustifolia Turcz., S. repens var. latifolia Turcz., and one form (Silene repens f. densa Kom. are lectotypified.Key words: Caryophyllaceae, Silenoideae, type specimens, typification, Komarov Botanical Institute (LE, Siberia, Far East. 

  13. A new species of Glaphyropoma: the first subterranean copionodontine catfish and the first occurrence of opercular odontodes in the subfamily (Siluriformes: Trichomycteridae

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    Maria Elina Bichuette

    Full Text Available A new species of the rare copionodontine genus Glaphyropoma is described from subterranean waters in the Diamantina Plateau, Bahia State, central northeastern Brazil. This is the first troglomorphic species in the subfamily Copionodontinae. It is distinguished from all other copionodontines by the presence of opercular odontodes, and further distinguished from its only congener, G. rodriguesi, by the reduction of dark integumentary pigmentation. The new species shares the single synapomorphy previously proposed for Glaphyropoma, the marked narrowing of the first hypobranchial and indirect character evidence also supports its inclusion in the genus. The presence of opercular odontodes in the new species, in combination with a reviewed hypothesis of sister group relationship between Copionodontinae and Trichogeninae, indicate that the absence of opercular odontodes in previously-known copionodontines is secondary, rather than primitive.

  14. A novel toxin from the venom of the scorpion Tityus trivittatus, is the first member of a new alpha-KTX subfamily.

    Science.gov (United States)

    Abdel-Mottaleb, Yousra; Coronas, Fredy V; de Roodt, Adolfo R; Possani, Lourival D; Tytgat, Jan

    2006-01-23

    The first example of a new sub-family of toxins (alpha-KTx20.1) from the scorpion Tityus trivittatus was purified, sequenced and characterized physiologically. It has 29 amino acid residues, three disulfide bridges assumed to adopt the cysteine-stabilized alpha/beta scaffold with a pI value of 8.98. The sequence identities with all the other known alpha-KTx are less than 40%. Its effects were verified using seven different cloned K(+) channels (vertebrate Kv1.1-1.5, Shaker IR and hERG) expressed in Xenopus leavis oocytes. The toxin-induced effects show large differences among the different K(+) channels and a preference towards Kv1.3 (EC50=7.9+/-1.4 nM).

  15. Comparative analysis of the male reproductive accessory glands of bat species from the five Brazilian subfamilies of the family Phyllostomidae (Chiroptera).

    Science.gov (United States)

    Martins, Fabiane F; Puga, Cintia C I; Beguelini, Mateus R; Morielle-Versute, Eliana; Vilamaior, Patricia S L; Taboga, Sebastião R

    2015-04-01

    This study aimed to morphologically characterize and compare the male reproductive accessory glands (RAGs) of bats belonging to the five Brazilian subfamilies of the family Phyllostomidae (Carollia perspicillata-Carollinae; Desmodus rotundus-Desmodontinae; Glossophaga soricina-Glossophaginae; Phyllostomus discolor-Phyllostominae and Platyrrhinus lineatus-Stenodermatinae). The study demonstrated that the RAGs of phyllostomid bats were comprised of a pair of extra-abdominal bulbourethral glands and an intra-abdominal complex, composed of paraurethral glands and a prostate with two (Desmodontinae and Stenodermatinae) or three (Carollinae, Glossophaginae and Phyllostominae) different regions, with the absence of the seminal vesicles; this pattern possibly evolved from a process of compaction of the prostatic regions from an ancestor with three regions.

  16. Structure, Function, and Evolution of Rice Centromeres

    Energy Technology Data Exchange (ETDEWEB)

    Jiang, Jiming

    2010-02-04

    The centromere is the most characteristic landmark of eukaryotic chromosomes. Centromeres function as the site for kinetochore assembly and spindle attachment, allowing for the faithful pairing and segregation of sister chromatids during cell division. Characterization of centromeric DNA is not only essential to understand the structure and organization of plant genomes, but it is also a critical step in the development of plant artificial chromosomes. The centromeres of most model eukaryotic species, consist predominantly of long arrays of satellite DNA. Determining the precise DNA boundary of a centromere has proven to be a difficult task in multicellular eukaryotes. We have successfully cloned and sequenced the centromere of rice chromosome 8 (Cen8), representing the first fully sequenced centromere from any multicellular eukaryotes. The functional core of Cen8 spans ~800 kb of DNA, which was determined by chromatin immunoprecipitation (ChIP) using an antibody against the rice centromere-specific H3 histone. We discovered 16 actively transcribed genes distributed throughout the Cen8 region. In addition to Cen8, we have characterized eight additional rice centromeres using the next generation sequencing technology. We discovered four subfamilies of the CRR retrotransposon that is highly enriched in rice centromeres. CRR elements are constitutively transcribed and different CRR subfamilies are differentially processed by RNAi. These results suggest that different CRR subfamilies may play different roles in the RNAi-mediated pathway for formation and maintenance of centromeric chromatin.

  17. Identification and initial characterization of the 3' end of gene transcripts encoding putative members of the pheromone receptor subfamily in Lepidoptera

    Institute of Scientific and Technical Information of China (English)

    Stephen F. Garczynski; Kevin W. Wanner; Thomas R. Unruh

    2012-01-01

    Semiochemicals,including pheromones and kairomones,used in pest management programs reduce the need for chemical insecticides,and understanding their interactions with their membrane receptors may help make them more effective in the field.Identification of odorant receptors in the Lepidoptera has mainly been achieved using bioinformatics to search DNA sequences generated by genome or expressed sequence tag (EST) sequencing projects.This study reports a rapid method to identify members of the pheromone receptor subfamily in Lepidoptera.Degenerate oligonucleotide primers were designed against a conserved amino acid sequence in the carboxyl terminus of known lepidopteran pheromone receptors,and the primers were used in a 3' rapid amplification of complementary DNA (cDNA) ends procedure.Polymerase chain reaction products generated from seven different lepidopteran species were TA cloned and sequenced.The eDNA sequences of 25 transcripts were determined to encode potential members of the pheromone receptor subfamily.These cDNAs ranged from 238 to 642 bp and encoded 49-54 amino acids of the carboxyl terminus.Analysis of the 3' untranslated region reveals that most of the transcripts contain multiple polyadenylation signal sequences,and in the case ofManduca sexta,an alternate polyadenylation signal appears to be used in transcript processing.The 3' untranslated region was also useful in determining unique receptors encoded by transcripts having highly similar nucleotide and amino acid sequences.Overall,this technique provides a complementary method of pheromone receptor identification in EST sequencing projects,or can be used as a stand-alone method in conjunction with 5' rapid amplification of cDNA ends procedures.

  18. A multi-locus analysis of phylogenetic relationships within grass subfamily Pooideae (Poaceae) inferred from sequences of nuclear single copy gene regions compared with plastid DNA.

    Science.gov (United States)

    Hochbach, Anne; Schneider, Julia; Röser, Martin

    2015-06-01

    To investigate phylogenetic relationships within the grass subfamily Pooideae we studied about 50 taxa covering all recognized tribes, using one plastid DNA (cpDNA) marker (matK gene-3'trnK exon) and for the first time four nuclear single copy gene loci. DNA sequence information from two parts of the nuclear genes topoisomerase 6 (Topo6) spanning the exons 8-13 and 17-19, the exons 9-13 encoding plastid acetyl-CoA-carboxylase (Acc1) and the partial exon 1 of phytochrome B (PhyB) were generated. Individual and nuclear combined data were evaluated using maximum parsimony, maximum likelihood and Bayesian methods. All of the phylogenetic results show Brachyelytrum and the tribe Nardeae as earliest diverging lineages within the subfamily. The 'core' Pooideae (Hordeeae and the Aveneae/Poeae tribe complex) are also strongly supported, as well as the monophyly of the tribes Brachypodieae, Meliceae and Stipeae (except PhyB). The beak grass tribe Diarrheneae and the tribe Duthieeae are not monophyletic in some of the analyses. However, the combined nuclear DNA (nDNA) tree yields the highest resolution and the best delimitation of the tribes, and provides the following evolutionary hypothesis for the tribes: Brachyelytrum, Nardeae, Duthieeae, Meliceae, Stipeae, Diarrheneae, Brachypodieae and the 'core' Pooideae. Within the individual datasets, the phylogenetic trees obtained from Topo6 exon 8-13 shows the most interesting results. The divergent positions of some clone sequences of Ampelodesmos mauritanicus and Trikeraia pappiformis, for instance, may indicate a hybrid origin of these stipoid taxa. Copyright © 2015 Elsevier Inc. All rights reserved.

  19. Have giant lobelias evolved several times independently? Life form shifts and historical biogeography of the cosmopolitan and highly diverse subfamily Lobelioideae (Campanulaceae

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    Antonelli Alexandre

    2009-01-01

    Full Text Available Abstract Background The tendency of animals and plants to independently develop similar features under similar evolutionary pressures - convergence - is a widespread phenomenon in nature. In plants, convergence has been suggested to explain the striking similarity in life form between the giant lobelioids (Campanulaceae, the bellflower family of Africa and the Hawaiian Islands. Under this assumption these plants would have developed the giant habit from herbaceous ancestors independently, in much the same way as has been suggested for the giant senecios of Africa and the silversword alliance of Hawaii. Results Phylogenetic analyses based on plastid (rbcL, trnL-F and nuclear (internal transcribed spacer [ITS] DNA sequences for 101 species in subfamily Lobelioideae demonstrate that the large lobelioids from eastern Africa the Hawaiian Islands, and also South America, French Polynesia and southeast Asia, form a strongly supported monophyletic group. Ancestral state reconstructions of life form and distribution, taking into account phylogenetic uncertainty, indicate their descent from a woody ancestor that was probably confined to Africa. Molecular dating analyses using Penalized Likelihood and Bayesian relaxed clock approaches, and combining multiple calibration points, estimate their first diversification at ~25-33 million years ago (Ma, shortly followed by several long-distance dispersal events that resulted in the current pantropical distribution. Conclusion These results confidently show that lobelioid species, commonly called 'giant', are very closely related and have not developed their giant form from herbaceous ancestors independently. This study, which includes the hitherto largest taxon sampling for subfamily Lobelioideae, highlights the need for a broad phylogenetic framework for testing assumptions about morphological development in general, and convergent evolution in particular.

  20. Homology of the internal sac components in the leaf beetle subfamily Criocerinae and evolutionary novelties related to the extremely elongated flagellum.

    Science.gov (United States)

    Matsumura, Yoko; Yoshizawa, Kazunori

    2012-05-01

    Extremely elongated intromittent organs are found in a wide range of taxa, especially among insects. This phenomenon is generally thought to result from sexual selection, but it is predicted that limited storage space in the body cavity and the difficulty of using the elongated organs should have constrained the evolution of extreme elongation, neutralizing any selective advantage. Therefore, in groups with long intromittent organs, features that overcome these constraints may have evolved or coevolved together with intromittent organ elongation. Using a comparative morphological approach and outgroup comparisons, we identified potential constraints and key novelties that may neutralize such constraints in the leaf beetle subfamily Criocerinae. Observations of the internal sac structure throughout Criocerinae were performed. Comparing the results with preceding studies from outgroups, a ground plan of the criocerine internal sac was constructed. Our analysis also identified specific features that are always correlated with extreme elongation: the rotation of whole internal-sac sclerites and the possession of a pocket in which to store the elongated flagellum. The pocket is thought to be formed by the rotation of the sclerites, markedly altering internal sac shape from the criocerine ground plan. Onlythe clades that have acquired this derived state contain species with an elongated flagellum that distinctly exceeds the median lobe length. It is presumed that these character correlations evolved independently three times. The detected character correlations corroborate the hypothesis that there are latent adaptive constraints for the evolution of extremely elongated intromittent organs. The constraints may have been neutralized by the alteration from the criocerine ground plan resulting in the formation of a storage pocket. In conclusion, deviation from the criocerine ground plan is considered to be the evolutionary innovation that neutralized the latent adaptive

  1. A holistic phylogeny of the coronin gene family reveals an ancient origin of the tandem-coronin, defines a new subfamily, and predicts protein function

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    Kollmar Martin

    2011-09-01

    Full Text Available Abstract Background Coronins belong to the superfamily of the eukaryotic-specific WD40-repeat proteins and play a role in several actin-dependent processes like cytokinesis, cell motility, phagocytosis, and vesicular trafficking. Two major types of coronins are known: First, the short coronins consisting of an N-terminal coronin domain, a unique region and a short coiled-coil region, and secondly the tandem coronins comprising two coronin domains. Results 723 coronin proteins from 358 species have been identified by analyzing the whole-genome assemblies of all available sequenced eukaryotes (March 2011. The organisms analyzed represent most eukaryotic kingdoms but also cover every taxon several times to provide a better statistical sampling. The phylogenetic tree of the coronin domains based on the Bayesian method is in accordance with the most recent grouping of the major kingdoms of the eukaryotes and also with the grouping of more recently separated branches. Based on this "holistic" approach the coronins group into four classes: class-1 (Type I and class-2 (Type II are metazoan/choanoflagellate specific classes, class-3 contains the tandem-coronins (Type III, and the new class-4 represents the coronins fused to villin (Type IV. Short coronins from non-metazoans are equally related to class-1 and class-2 coronins and thus remain unclassified. Conclusions The coronin class distribution suggests that the last common eukaryotic ancestor possessed a single and a tandem-coronin, and most probably a class-4 coronin of which homologs have been identified in Excavata and Opisthokonts although most of these species subsequently lost the class-4 homolog. The most ancient short coronin already contained the trimerization motif in the coiled-coil domain.

  2. A systems biology approach identifies a R2R3 MYB gene subfamily with distinct and overlapping functions in regulation of aliphatic glucosinolates.

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    Ida Elken Sønderby

    Full Text Available BACKGROUND: Glucosinolates are natural metabolites in the order Brassicales that defend plants against both herbivores and pathogens and can attract specialized insects. Knowledge about the genes controlling glucosinolate regulation is limited. Here, we identify three R2R3 MYB transcription factors regulating aliphatic glucosinolate biosynthesis in Arabidopsis by combining several systems biology tools. METHODOLOGY/PRINCIPAL FINDINGS: MYB28 was identified as a candidate regulator of aliphatic glucosinolates based on its co-localization within a genomic region controlling variation both in aliphatic glucosinolate content (metabolite QTL and in transcript level for genes involved in the biosynthesis of aliphatic glucosinolates (expression QTL, as well as its co-expression with genes in aliphatic glucosinolate biosynthesis. A phylogenetic analysis with the R2R3 motif of MYB28 showed that it and two homologues, MYB29 and MYB76, were members of an Arabidopsis-specific clade that included three characterized regulators of indole glucosinolates. Over-expression of the individual MYB genes showed that they all had the capacity to increase the production of aliphatic glucosinolates in leaves and seeds and induce gene expression of aliphatic biosynthetic genes within leaves. Analysis of leaves and seeds of single knockout mutants showed that mutants of MYB29 and MYB76 have reductions in only short-chained aliphatic glucosinolates whereas a mutant in MYB28 has reductions in both short- and long-chained aliphatic glucosinolates. Furthermore, analysis of a double knockout in MYB28 and MYB29 identified an emergent property of the system since the absence of aliphatic glucosinolates in these plants could not be predicted by the chemotype of the single knockouts. CONCLUSIONS/SIGNIFICANCE: It seems that these cruciferous-specific MYB regulatory genes have evolved both overlapping and specific regulatory capacities. This provides a unique system within which to study the evolution of MYB regulatory factors and their downstream targets.

  3. Microarray Analysis Reveals Increased Expression of Matrix Metalloproteases and Cytokines of Interleukin-20 Subfamily in the Kidneys of Neonate Rats Underwent Unilateral Ureteral Obstruction: A Potential Role of IL-24 in the Regulation of Inflammation and Tissue Remodeling.

    Science.gov (United States)

    Pap, Domonkos; Sziksz, Erna; Kiss, Zoltán; Rokonay, Réka; Veres-Székely, Apor; Lippai, Rita; Takács, István Márton; Kis, Éva; Fekete, Andrea; Reusz, György; Vannay, Adam; Szabó, Attila J

    2017-01-01

    Congenital obstructive nephropathy (CON) is the main cause of pediatric chronic kidney diseases leading to renal fibrosis. High morbidity and limited treatment opportunities of CON urge the better understanding of the underlying molecular mechanisms. To identify the differentially expressed genes, microarray analysis was performed on the kidney samples of neonatal rats underwent unilateral ureteral obstruction (UUO). Microarray results were then validated by real-time RT-PCR and bioinformatics analysis was carried out to identify the relevant genes, functional groups and pathways involved in the pathomechanism of CON. Renal expression of matrix metalloproteinase (MMP)-12 and interleukin (IL)-24 were evaluated by real-time RT-PCR, flow cytometry and immunohistochemical analysis. Effect of the main profibrotic factors on the expression of MMP-12 and IL-24 was investigated on HK-2 and HEK-293 cell lines. Finally, the effect of IL-24 treatment on the expression of pro-inflammatory cytokines and MMPs were tested in vitro. Microarray analysis revealed 880 transcripts showing >2.0-fold change following UUO, enriched mainly in immune response related processes. The most up-regulated genes were MMPs and members of IL-20 cytokine subfamily, including MMP-3, MMP-7, MMP-12, IL-19 and IL-24. We found that while TGF-β treatment inhibits the expression of MMP-12 and IL-24, H2O2 or PDGF-B treatment induce the epithelial expression of MMP-12. We demonstrated that IL-24 treatment decreases the expression of IL-6 and MMP-3 in the renal epithelial cells. This study provides an extensive view of UUO induced changes in the gene expression profile of the developing kidney and describes novel molecules, which may play significant role in the pathomechanism of CON. © 2017 The Author(s)Published by S. Karger AG, Basel.

  4. Villin promoter-mediated transgenic expression of transient receptor potential cation channel, subfamily V, member 6 (TRPV6) increases intestinal calcium absorption in wild-type and vitamin D receptor knockout mice.

    Science.gov (United States)

    Cui, Min; Li, Qiang; Johnson, Robert; Fleet, James C

    2012-10-01

    Transient receptor potential cation channel, subfamily V, member 6 (TRPV6) is an apical membrane calcium (Ca) channel in the small intestine proposed to be essential for vitamin D-regulated intestinal Ca absorption. Recent studies have challenged the proposed role for TRPV6 in Ca absorption. We directly tested intestinal TRPV6 function in Ca and bone metabolism in wild-type (WT) and vitamin D receptor knockout (VDRKO) mice. TRPV6 transgenic mice (TG) were made with intestinal epithelium-specific expression of a 3X Flag-tagged human TRPV6 protein. TG and VDRKO mice were crossed to make TG-VDRKO mice. Ca and bone metabolism was examined in WT, TG, VDRKO, and TG-VDRKO mice. TG mice developed hypercalcemia and soft tissue calcification on a chow diet. In TG mice fed a 0.25% Ca diet, Ca absorption was more than three-fold higher and femur bone mineral density (BMD) was 26% higher than WT. Renal 1α hydroxylase (CYP27B1) mRNA and intestinal expression of the natural mouse TRPV6 gene were reduced to intestine calbindin-D(9k) expression was elevated >15 times in TG mice. TG-VDRKO mice had high Ca absorption that prevented the low serum Ca, high renal CYP27B1 mRNA, low BMD, and abnormal bone microarchitecture seen in VDRKO mice. In addition, small intestinal calbindin D(9K) mRNA and protein levels were elevated in TG-VDRKO. Transgenic TRPV6 expression in intestine is sufficient to increase Ca absorption and bone density, even in VDRKO mice. VDR-independent upregulation of intestinal calbindin D(9k) in TG-VDRKO suggests this protein may buffer intracellular Ca during Ca absorption. © 2012 American Society for Bone and Mineral Research.

  5. Molecular properties of the class III subfamily of acyl-coenyzme A binding proteins from tung tree (Vernicia fordii)

    Science.gov (United States)

    Acyl-CoA binding proteins (ACBPs) have been identified in most branches of life. A single prototypical ACBP was first discovered in yeast, and was found to play a signficant role in lipid metabolism, among other functions. Plants also contain the prototype small, soluble ACBP, but have also evolve...

  6. Identification and characterization of four Chrystanthemum MADS-box genes, belonging to the APETALA1/FRUIFULL and SEPALLATA3 subfamilies

    NARCIS (Netherlands)

    Shchennikova, A.V.; Shulga, O.A.; Immink, R.; Skryabin, K.G.; Angenent, G.C.

    2004-01-01

    Four full-length MADS-box cDNAs from chrysanthemum, designated Chrysanthemum Dendrathema grandiflorum MADS (CDM) 8, CDM41, CDM111, and CDM44, have been isolated and further functionally characterized. Protein sequence alignment and expression patterns of the corresponding genes suggest that CDM8 and

  7. Identification and characterization of four chrysanthemum MADS-box genes, belonging to the APETALA1/FRUITFULL and SEPALLATA3 subfamilies

    NARCIS (Netherlands)

    Shchennikova, A.V.; Shulga, O.A.; Immink, R.; Skryabin, K.G.; Angenent, G.C.

    2004-01-01

    Four full-length MADS-box cDNAs from chrysanthemum, designated Chrysanthemum Dendrathema grandiflorum MADS (CDM) 8, CDM41, CDM111, and CDM44, have been isolated and further functionally characterized. Protein sequence alignment and expression patterns of the corresponding genes suggest that CDM8 and

  8. Function and regulation of the channel-kinase TRPM7 in health and disease

    NARCIS (Netherlands)

    Visser, D.; Middelbeek, J.; Leeuwen, F.N. van; Jalink, K.

    2014-01-01

    Transient receptor potential (TRP) cation channels represent a large and diverse family of ion channels that act as important transducers of sensory information. The Melastatin subfamily member TRPM7 has garnered much interest due to its functional kinase domain; a unique feature among ion channels.

  9. Leaf and stem CO/sub 2/ uptake in the three subfamilies of the Cactaceae. [Pereskia aculeata; Pereskia grandifolia; Maihuenia poeppigii; Carnegiea gigantea; Ferocactus acanthodes; Coryphantha vivipara; Mammillaria dioica; Opuntia ficus-inidica; Pereskiopsis porteri; Quiabentia chacoensis; Austrocylindropuntia subulata

    Energy Technology Data Exchange (ETDEWEB)

    Nobel, P.S.; Hartsock, T.L.

    1986-04-01

    Net CO/sub 2/ uptake over 24-hour periods was examined for the leaves and for the stems of 11 species of cacti representing all three subfamilies. For Pereskia aculeata, Pereskia grandifolia, and Maihuenia poeppigii (subfamily Pereskioideae), all the net shoot CO/sub 2/ uptake was by the leaves and during the daytime. In contrast, for the leafless species Carnegiea gigantea, Ferocactus acanthodes, Coryphantha vivipara, and Mammillaria dioica (subfamily Cactoideae), all the shoot net CO/sub 2/ uptake was by the stems and at night. Similarly, for leafless Opuntia ficus-indica (subfamily Opuntioideae), all net CO/sub 2/ uptake occurred at night. For leafy members of the Opuntioideae (Pereskiopsis porteri, Quiabentia chacoensis, Austrocylindropuntia subulata), at least 88% of the shoot CO/sub 2/ uptake over 24 hours was by the leaves and some CO/sub 2/ uptake occurred at night. Leaves responded to the instantaneous level of photosynthetically active radiation (PAR) during the daytime, as occurs for C/sub 3/ plants, whereas nocturnal CO/sub 2/ uptake by stems of O. ficus-indica and F. acanthodes responded to the total daily PAR, as occurs for Crassulacean acid metabolism (CAM) plants. Thus, under the well-watered conditions employed, the Pereskioideae behaved as C/sub 3/ plants, the Cactoideae behaved as CAM plants, and the Opuntioideae exhibited characteristics of both pathways.

  10. A novel cluster of mariner-like elements belonging to mellifera subfamily from spiders and insects: implications of recent horizontal transfer on the South-West Islands of Japan.

    Science.gov (United States)

    Yamada, Kaori; Kawanishi, Yuichi; Yamada, Akinori; Tokuda, Gaku; Gurung, Raj Deep; Sasaki, Takeshi; Nakajima, Yumiko; Maekawa, Hideaki

    2014-04-01

    Mariner-like elements (MLEs) have been isolated from various eukaryotic genomes and they are divided into 15 subfamilies, including main five subfamilies: mauritiana, cecropia, mellifera/capitata, irritans, and elegans/briggsae. In the present study, MLEs belonging to mellifera subfamily were isolated from various spiders and insects (Hymenoptera and Lepidoptera) inhabiting the South-West Islands of Japan and neighboring regions. MLEs isolated from 15 different species formed a distinct novel cluster in mellifera subfamily. MLEs obtained from three different species [i.e., the bee Amegilla senahai subflavescens (Amsmar1), the wasp Campsomeris sp. (Casmar1), and the swallowtail butterfly Pachliopta aristolochiae (Paamar1)] contained an intact open reading frame that encoded a putative transposase. These transposases exhibited high similarity of 97.9% among themselves. In case of Casmar1, the presence of an intact ORF was found in high frequencies (i.e., 11 out of 12 clones). In addition, these transposases also showed the presence of a terminal inverted repeat-binding motif, DD(34)D and two highly conserved amino acid motifs, (W/L)(I/L)PHQL and YSP(D/N)L(A/S)P. These two motifs differed from previously known motifs, WVPHEL and YSPDLAP. MLEs isolated from these three different species may have been inserted into their genomes by horizontal transfer. Furthermore, the presence of an intact ORF suggests that they are still active in habitats along these isolated islands.

  11. A distinct subfamily of papain-like cystein proteinases regulated by senescence and stresses in Glycine max.

    Science.gov (United States)

    Esteban-García, Belén; Garrido-Cárdenas, José Antonio; Alonso, Diego López; García-Maroto, Federico

    2010-09-01

    GMCP3 encodes a cystein proteinase of Glycine max belonging to the papain-like family (C1A in MEROPS database) that was previously found to be involved in the mobilization of protein reserves during seed germination. Here, we report that GMCP3 is induced by senescence and diverse stresses in non-seed tissues, thus indicating a more general function in plants. Cladistic analysis of papain-like proteins of plants indicated that GMCP3, along with related proteases of other species, belongs to a distinct new group within the C1A family, which can also be distinguished by the four-exon structure of the gene. We also describe the genomic organization of GMCP3 revealing the presence of two closely related copies that are transcriptionally regulated in a similar way, although only one appears to be functional.

  12. Chilean Pitavia more closely related to Oceania and Old World Rutaceae than to Neotropical groups: evidence from two cpDNA non-coding regions, with a new subfamilial classification of the family.

    Science.gov (United States)

    Groppo, Milton; Kallunki, Jacquelyn A; Pirani, José Rubens; Antonelli, Alexandre

    2012-01-01

    The position of the plant genus Pitavia within an infrafamilial phylogeny of Rutaceae (rue, or orange family) was investigated with the use of two non-coding regions from cpDNA, the trnL-trnF region and the rps16 intron. The only species of the genus, Pitavia punctata Molina, is restricted to the temperate forests of the Coastal Cordillera of Central-Southern Chile and threatened by loss of habitat. The genus traditionally has been treated as part of tribe Zanthoxyleae (subfamily Rutoideae) where it constitutes the monogeneric tribe Pitaviinae. This tribe and genus are characterized by fruits of 1 to 4 fleshy drupelets, unlike the dehiscent fruits typical of the subfamily. Fifty-five taxa of Rutaceae, representing 53 genera (nearly one-third of those in the family) and all subfamilies, tribes, and almost all subtribes of the family were included. Parsimony and Bayesian inference were used to infer the phylogeny; six taxa of Meliaceae, Sapindaceae, and Simaroubaceae, all members of Sapindales, were also used as out-groups. Results from both analyses were congruent and showed Pitavia as sister to Flindersia and Lunasia, both genera with species scattered through Australia, Philippines, Moluccas, New Guinea and the Malayan region, and phylogenetically far from other Neotropical Rutaceae, such as the Galipeinae (Galipeeae, Rutoideae) and Pteleinae (Toddalieae, former Toddalioideae). Additionally, a new circumscription of the subfamilies of Rutaceae is presented and discussed. Only two subfamilies (both monophyletic) are recognized: Cneoroideae (including Dictyolomatoideae, Spathelioideae, Cneoraceae, and Ptaeroxylaceae) and Rutoideae (including not only traditional Rutoideae but also Aurantioideae, Flindersioideae, and Toddalioideae). As a consequence, Aurantioideae (Citrus and allies) is reduced to tribal rank as Aurantieae.

  13. Chilean Pitavia more closely related to Oceania and Old World Rutaceae than to Neotropical groups: evidence from two cpDNA non-coding regions, with a new subfamilial classification of the family

    Directory of Open Access Journals (Sweden)

    Milton Groppo

    2012-12-01

    Full Text Available The position of the plant genus Pitavia within an infrafamilial phylogeny of Rutaceae (rue, or orange family was investigated with the use of two non-coding regions from cpDNA, the trnL-trnF region and the rps16 intron. The only species of the genus, Pitavia punctata Molina, is restricted to the temperate forests of the Coastal Cordillera of Central-Southern Chile and threatened by loss of habitat. The genus traditionally has been treated as part of tribe Zanthoxyleae (subfamily Rutoideae where it constitutes the monogeneric tribe Pitaviinae. This tribe and genus are characterized by fruits of 1 to 4 fleshy drupelets, unlike the dehiscent fruits typical of the subfamily. Fifty-five taxa of Rutaceae, representing 53 genera (nearly one-third of those in the family and all subfamilies, tribes, and almost all subtribes of the family were included. Parsimony and Bayesian inference were used to infer the phylogeny; six taxa of Meliaceae, Sapindaceae, and Simaroubaceae, all members of Sapindales, were also used as out-groups. Results from both analyses were congruent and showed Pitavia as sister to Flindersia and Lunasia, both genera with species scattered through Australia, Philippines, Moluccas, New Guinea and the Malayan region, and phylogenetically far from other Neotropical Rutaceae, such as the Galipeinae (Galipeeae, Rutoideae and Pteleinae (Toddalieae, former Toddalioideae. Additionally, a new circumscription of the subfamilies of Rutaceae is presented and discussed. Only two subfamilies (both monophyletic are recognized: Cneoroideae (including Dictyolomatoideae, Spathelioideae, Cneoraceae, and Ptaeroxylaceae and Rutoideae (including not only traditional Rutoideae but also Aurantioideae, Flindersioideae, and Toddalioideae. As a consequence, Aurantioideae (Citrus and allies is reduced to tribal rank as Aurantieae.

  14. Functional Analyses of Resurrected and Contemporary Enzymes Illuminate an Evolutionary Path for the Emergence of Exolysis in Polysaccharide Lyase Family 2.

    Science.gov (United States)

    McLean, Richard; Hobbs, Joanne K; Suits, Michael D; Tuomivaara, Sami T; Jones, Darryl R; Boraston, Alisdair B; Abbott, D Wade

    2015-08-28

    Family 2 polysaccharide lyases (PL2s) preferentially catalyze the β-elimination of homogalacturonan using transition metals as catalytic cofactors. PL2 is divided into two subfamilies that have been generally associated with secretion, Mg(2+) dependence, and endolysis (subfamily 1) and with intracellular localization, Mn(2+) dependence, and exolysis (subfamily 2). When present within a genome, PL2 genes are typically found as tandem copies, which suggests that they provide complementary activities at different stages along a catabolic cascade. This relationship most likely evolved by gene duplication and functional divergence (i.e. neofunctionalization). Although the molecular basis of subfamily 1 endolytic activity is understood, the adaptations within the active site of subfamily 2 enzymes that contribute to exolysis have not been determined. In order to investigate this relationship, we have conducted a comparative enzymatic analysis of enzymes dispersed within the PL2 phylogenetic tree and elucidated the structure of VvPL2 from Vibrio vulnificus YJ016, which represents a transitional member between subfamiles 1 and 2. In addition, we have used ancestral sequence reconstruction to functionally investigate the segregated evolutionary history of PL2 progenitor enzymes and illuminate the molecular evolution of exolysis. This study highlights that ancestral sequence reconstruction in combination with the comparative analysis of contemporary and resurrected enzymes holds promise for elucidating the origins and activities of other carbohydrate active enzyme families and the biological significance of cryptic metabolic pathways, such as pectinolysis within the zoonotic marine pathogen V. vulnificus.

  15. Functional Diversity of Fibroblast Growth Factors in Bone Formation

    Directory of Open Access Journals (Sweden)

    Yuichiro Takei

    2015-01-01

    Full Text Available The functional significance of fibroblast growth factor (FGF signaling in bone formation has been demonstrated through genetic loss-of-function and gain-of-function approaches. FGFs, comprising 22 family members, are classified into three subfamilies: canonical, hormone-like, and intracellular. The former two subfamilies activate their signaling pathways through FGF receptors (FGFRs. Currently, intracellular FGFs appear to be primarily involved in the nervous system. Canonical FGFs such as FGF2 play significant roles in bone formation, and precise spatiotemporal control of FGFs and FGFRs at the transcriptional and posttranscriptional levels may allow for the functional diversity of FGFs during bone formation. Recently, several research groups, including ours, have shown that FGF23, a member of the hormone-like FGF subfamily, is primarily expressed in osteocytes/osteoblasts. This polypeptide decreases serum phosphate levels by inhibiting renal phosphate reabsorption and vitamin D3 activation, resulting in mineralization defects in the bone. Thus, FGFs are involved in the positive and negative regulation of bone formation. In this review, we focus on the reciprocal roles of FGFs in bone formation in relation to their local versus systemic effects.

  16. Gating currents from a Kv3 subfamily potassium channel: charge movement and modification by BDS-II toxin.

    Science.gov (United States)

    Wang, Zhuren; Robertson, Brian; Fedida, David

    2007-11-01

    Kv3 channels have a major role in determining neuronal excitability, and are characterized by ultra-rapid kinetics of gating and a high activation threshold. However, the gating currents, which occur as a result of positional changes of the charged elements in the channel structure during activation, are not well understood. Here we report a study of gating currents from wild-type Kv3.2b channels, expressed in human embryonic kidney (HEK) cells to facilitate high time-resolution recording. On-gating currents (I(g,on)) had extremely rapid kinetics such that at +80 mV, the time constant for the decay of I(g,on) was only approximately 0.3 ms. Decay of I(g,on) appeared mono-exponential at all potentials studied, and in support of this, the charge-voltage (Q-V) relationship was fitted with a single Boltzmann function, supporting the idea that only one charge system is required to account for the time course of I(g,on) and the voltage dependence of Q(on). The voltage (V((1/2))) for half movement of gating charge was -8.4 +/- 4.0 mV (n = 6), which closely matches the voltage dependence of activation of Kv3.2b ionic currents reported before. Depolarizations to more positive potentials than 0 mV decreased the amplitude and slowed the decay of the off-gating currents (I(g,off)), suggesting that a rate-limiting step in opening was present in Kv3 channels as in Shaker and other Kv channels. Return of charge was negatively shifted along the potential axis with a V((1/2)) of Q(off) of -80.9 +/- 0.8 mV (n = 3), which allowed approximately 90% charge return upon repolarization to -100 mV. BDS-II toxin apparently reduced I(g,on), and greatly slowed the kinetics of I(g,on), while shifting the Q-V relationship in the depolarizing direction. However, the Q-V relationship remained well fitted by a single Boltzmann function. These data provide the first description of Kv3 gating currents and give further insight into the interaction of BDS toxins and Kv3 channels.

  17. Afatinib reverses multidrug resistance in ovarian cancer via dually inhibiting ATP binding cassette subfamily B member 1.

    Science.gov (United States)

    Wang, Sheng-qi; Liu, Shi-ting; Zhao, Bo-xin; Yang, Fu-heng; Wang, Ya-tian; Liang, Qian-Ying; Sun, Ya-bin; Liu, Yuan; Song, Zhi-hua; Cai, Yun; Li, Guo-feng

    2015-09-22

    ABCB1-mediated multidrug resistance (MDR) remains a major obstacle to successful chemotherapy in ovarian cancer. Herein, afatinib at nontoxic concentrations significantly reversed ABCB1-mediated MDR in ovarian cancer cells in vitro (p afatinib caused tumor regressions and tumor necrosis in A2780T xenografts in vivo. More interestingly, unlike reversible TKIs, afatinib had a distinctive dual-mode action. Afatinib not only inhibited the efflux function of ABCB1, but also attenuated its expression transcriptionally via down-regulation of PI3K/AKT and MAPK/p38-dependent activation of NF-κB. Furthermore, apart from a substrate binding domain, afatinib could also bind to an ATP binding domain of ABCB1 through forming hydrogen bonds with Gly533, Gly534, Lys536 and Ala560 sites. Importantly, mutations in these four binding sites of ABCB1 and the tyrosine kinase domain of EGFR were not correlated with the reversal activity of afatinib on MDR. Given that afatinib is a clinically approved drug, our results suggest combining afatinib with chemotherapeutic drugs in ovarian cancer. This study can facilitate the rediscovery of superior MDR reversal agents from molecular targeted drugs to provide a more effective and safer way of resensitizing MDR.

  18. Molecular Insights into the Klotho-Dependent, Endocrine Mode of Action of Fibroblast Growth Factor 19 Subfamily Members

    Energy Technology Data Exchange (ETDEWEB)

    Goetz,R.; Beenken, A.; Ibrahimi, O.; Kalinina, J.; Olsen, S.; Eliseenkova, A.; Xu, C.; Neubert, T.; Zhang, F.; et al.

    2007-01-01

    Unique among fibroblast growth factors (FGFs), FGF19, -21, and -23 act in an endocrine fashion to regulate energy, bile acid, glucose, lipid, phosphate, and vitamin D homeostasis. These FGFs require the presence of Klotho/{beta}Klotho in their target tissues. Here, we present the crystal structures of FGF19 alone and FGF23 in complex with sucrose octasulfate, a disaccharide chemically related to heparin. The conformation of the heparin-binding region between {beta} strands 10 and 12 in FGF19 and FGF23 diverges completely from the common conformation adopted by paracrine-acting FGFs. A cleft between this region and the {beta}1-{beta}2 loop, the other heparin-binding region, precludes direct interaction between heparin/heparan sulfate and backbone atoms of FGF19/23. This reduces the heparin-binding affinity of these ligands and confers endocrine function. Klotho/{beta}Klotho have evolved as a compensatory mechanism for the poor ability of heparin/heparan sulfate to promote binding of FGF19, -21, and -23 to their cognate receptors.

  19. Molecular insights into the klotho-dependent, endocrine mode of action of fibroblast growth factor 19 subfamily members.

    Science.gov (United States)

    Goetz, Regina; Beenken, Andrew; Ibrahimi, Omar A; Kalinina, Juliya; Olsen, Shaun K; Eliseenkova, Anna V; Xu, ChongFeng; Neubert, Thomas A; Zhang, Fuming; Linhardt, Robert J; Yu, Xijie; White, Kenneth E; Inagaki, Takeshi; Kliewer, Steven A; Yamamoto, Masaya; Kurosu, Hiroshi; Ogawa, Yasushi; Kuro-o, Makoto; Lanske, Beate; Razzaque, Mohammed S; Mohammadi, Moosa

    2007-05-01

    Unique among fibroblast growth factors (FGFs), FGF19, -21, and -23 act in an endocrine fashion to regulate energy, bile acid, glucose, lipid, phosphate, and vitamin D homeostasis. These FGFs require the presence of Klotho/betaKlotho in their target tissues. Here, we present the crystal structures of FGF19 alone and FGF23 in complex with sucrose octasulfate, a disaccharide chemically related to heparin. The conformation of the heparin-binding region between beta strands 10 and 12 in FGF19 and FGF23 diverges completely from the common conformation adopted by paracrine-acting FGFs. A cleft between this region and the beta1-beta2 loop, the other heparin-binding region, precludes direct interaction between heparin/heparan sulfate and backbone atoms of FGF19/23. This reduces the heparin-binding affinity of these ligands and confers endocrine function. Klotho/betaKlotho have evolved as a compensatory mechanism for the poor ability of heparin/heparan sulfate to promote binding of FGF19, -21, and -23 to their cognate receptors.

  20. Role of NH{sub 2}-terminal hydrophobic motif in the subcellular localization of ATP-binding cassette protein subfamily D: Common features in eukaryotic organisms

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Asaka; Asahina, Kota; Okamoto, Takumi; Kawaguchi, Kosuke [Department of Biological Chemistry, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194 (Japan); Kostsin, Dzmitry G. [Department of Biological Chemistry, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194 (Japan); Institute of Biophysics and Cell Engineering, National Academy of Sciences of Belarus, Academicheskaya Str. 27, Minsk 220072 (Belarus); Kashiwayama, Yoshinori [Department of Biological Chemistry, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194 (Japan); Takanashi, Kojiro; Yazaki, Kazufumi [Laboratory of Plant Gene Expression, Research Institute for Sustainable Humanosphere, Kyoko University, Uji, Kyoto 611-0011 (Japan); Imanaka, Tsuneo, E-mail: imanaka@pha.u-toyama.ac.jp [Department of Biological Chemistry, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194 (Japan); Morita, Masashi [Department of Biological Chemistry, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194 (Japan)

    2014-10-24

    Highlights: • ABCD proteins classifies based on with or without NH{sub 2}-terminal hydrophobic segment. • The ABCD proteins with the segment are targeted peroxisomes. • The ABCD proteins without the segment are targeted to the endoplasmic reticulum. • The role of the segment in organelle targeting is conserved in eukaryotic organisms. - Abstract: In mammals, four ATP-binding cassette (ABC) proteins belonging to subfamily D have been identified. ABCD1–3 possesses the NH{sub 2}-terminal hydrophobic region and are targeted to peroxisomes, while ABCD4 lacking the region is targeted to the endoplasmic reticulum (ER). Based on hydropathy plot analysis, we found that several eukaryotes have ABCD protein homologs lacking the NH{sub 2}-terminal hydrophobic segment (H0 motif). To investigate whether the role of the NH{sub 2}-terminal H0 motif in subcellular localization is conserved across species, we expressed ABCD proteins from several species (metazoan, plant and fungi) in fusion with GFP in CHO cells and examined their subcellular localization. ABCD proteins possessing the NH{sub 2}-terminal H0 motif were localized to peroxisomes, while ABCD proteins lacking this region lost this capacity. In addition, the deletion of the NH{sub 2}-terminal H0 motif of ABCD protein resulted in their localization to the ER. These results suggest that the role of the NH{sub 2}-terminal H0 motif in organelle targeting is widely conserved in living organisms.

  1. A New Subfamily of Sucrose Transporters, SUT4, with Low Affinity/High Capacity Localized in Enucleate Sieve Elements of Plants

    Science.gov (United States)

    Weise, Andreas; Barker, Laurence; Kühn, Christina; Lalonde, Sylvie; Buschmann, Henrik; Frommer, Wolf B.; Ward, John M.

    2000-01-01

    A new subfamily of sucrose transporters from Arabidopsis (AtSUT4), tomato (LeSUT4), and potato (StSUT4) was isolated, demonstrating only 47% similarity to the previously characterized SUT1. SUT4 from two plant species conferred sucrose uptake activity when expressed in yeast. The Km for sucrose uptake by AtSUT4 of 11.6 ± 0.6 mM was ∼10-fold greater than for all other plant sucrose transporters characterized to date. An ortholog from potato had similar kinetic properties. Thus, SUT4 corresponds to the low-affinity/high-capacity saturable component of sucrose uptake found in leaves. In contrast to SUT1, SUT4 is expressed predominantly in minor veins in source leaves, where high-capacity sucrose transport is needed for phloem loading. In potato and tomato, SUT4 was immunolocalized specifically to enucleate sieve elements, indicating that like SUT1, macromolecular trafficking is required to transport the mRNA or the protein from companion cells through plasmodesmata into the sieve elements. PMID:10948254

  2. A systematic review of the subfamily Syringophilinae (Acari: Syringophilidae) of the Nearctic region. Part 1: quill mites associated with passerines (Aves: Passeriformes).

    Science.gov (United States)

    Skoracki, Maciej; Spicer, Greg S; Oconnor, Barry M

    2016-02-29

    Quill mites belonging to the subfamily Syringophilinae Lavoipierre, 1953 associated with the Nearctic passeriform birds are revised. All of the 49 known species, which are grouped in seven genera, are recorded. Among them, four new species are described: Syringophiloidus audubioni sp. nov. from Spizella breweri (Cassini) (Emberizidae), Syringophilopsis catesbyi sp. nov. from Vireo olivaceus (Linnaeus) (Vireonidae), S. wilsoni sp. nov. from Pheucticus melanocephalus (Swainson) (Cardinalidae), and S. bartrami sp. nov. from Spizella passerina (Bechstein) (Emberizidae). The species Syringophilopsis hylocichlae Clark, 1964 syn. nov. is synonymized with Syringophilopsis turdus (Fritsch, 1958), and Syringophiloidus zonotrichia syn. nov. is synonymized with Betasyringophiloidus seiuri (Clark, 1964) comb. nov. Six species are recorded from the Nearctic region for the first time: Syringophiloidus delichonum Bochkov, 2001, S. glandarii (Fritsch, 1958), S. weiszii Skoracki et al., 2001, S. bombycillae Skoracki, 2002, Syringophilopsis mimidus Sikora et al., 2011, and Torotrogla merulae Skoracki et al., 2000. Data on Nearctic syringophiline species, their hosts and distribution are summarized and the keys to all species are constructed.

  3. Giant panda (Ailuropoda melanoleuca) population dynamics and bamboo (subfamily Bambusoideae) life history: a structured population approach to examining carrying capacity when the prey are semelparous

    Science.gov (United States)

    Carter, J.; Ackleh, A.S.; Leonard, B.P.; Wang, Hongfang

    1999-01-01

    The giant panda, Ailuropoda melanoleuca, is a highly specialized Ursid whose diet consists almost entirely of various species of bamboo. Bamboo (Bambusoideae) is a grass subfamily whose species often exhibit a synchronous semelparity. Synchronous semelparity can create local drops in carrying capacity for the panda. We modeled the interaction of pandas and their bamboo food resources with an age structured panda population model linked to a natural history model of bamboo biomass dynamics based on literature values of bamboo biomass, and giant panda life history dynamics. This paper reports the results of our examination of the interaction between pandas and their bamboo food resource and its implications for panda conservation. In the model all panda populations were well below the carrying capacity of the habitat. The giant panda populations growth was most sensitive to changes in birth rates and removal of reproductive aged individuals. Periodic starvation that has been documented in conjunction with bamboo die-offs is probably related to the inability to move to other areas within the region where bamboo is still available. Based on the results of this model, giant panda conservation should concentrate on keeping breeding individuals in the wild, keep corridors to different bamboo species open to pandas, and to concentrate research on bamboo life history.

  4. Physical mapping of 18S and 5S rDNA loci and histone H3 gene in grasshopper species of the subfamily Gomphocerinae (Acrididae).

    Science.gov (United States)

    Silva-Neto, L C; Bernardino, A C S; Loreto, V; Moura, R C

    2015-11-25

    In this study, fluorescence in situ hybridization (FISH) analysis was used to determine and compare the numbers and chromosomal locations of two multigene families (rDNA and histone H3) in four Neotropical species of gomphocerine grasshoppers. FISH using the 18S rDNA probe identified a single site on the S9 chromosome of Amblytropidia sp and Cauratettix borelli, a single site on chromosome M6 of Compsacris pulcher, and two sites (chromosomes L1 and L2) in Orphulella punctata. By contrast, FISH with a 5S rDNA probe identified dispersion of this sequence in the genomes of the four species, with evidence of intraspecific variations. Amblytropidia sp had six to eight FISH signals on autosomal chromosomes, while C. pulcher exhibited a signal only on the M5 bivalent. The histone H3 gene was less variable and was restricted to a single pair in all species. The conservation of the numbers and locations of 18S rDNA and H3 genes in conjunction with data from the literature was useful for evaluating karyotype evolution in this subfamily. The variation in the number and sizes of 5S rDNA sites indicates a process of recent dispersion that might have been mediated by transposition.

  5. Homodimerization Controls the Fibroblast Growth Factor 9 Subfamily's Receptor Binding and Heparan Sulfate-Dependent Diffusion in the Extracellular Matrix

    Energy Technology Data Exchange (ETDEWEB)

    Kalinina, J.; Byron, S; Makarenkova, H; Olsen, S; Eliseenkova, A; Larochelle, W; Dhanabal, M; Blais, S; Mohammadi, M; et. al.

    2009-01-01

    Uncontrolled fibroblast growth factor (FGF) signaling can lead to human diseases, necessitating multiple layers of self-regulatory control mechanisms to keep its activity in check. Herein, we demonstrate that FGF9 and FGF20 ligands undergo a reversible homodimerization, occluding their key receptor binding sites. To test the role of dimerization in ligand autoinhibition, we introduced structure-based mutations into the dimer interfaces of FGF9 and FGF20. The mutations weakened the ability of the ligands to dimerize, effectively increasing the concentrations of monomeric ligands capable of binding and activating their cognate FGF receptor in vitro and in living cells. Interestingly, the monomeric ligands exhibit reduced heparin binding, resulting in their increased radii of heparan sulfate-dependent diffusion and biologic action, as evidenced by the wider dilation area of ex vivo lung cultures in response to implanted mutant FGF9-loaded beads. Hence, our data demonstrate that homodimerization autoregulates FGF9 and FGF20's receptor binding and concentration gradients in the extracellular matrix. Our study is the first to implicate ligand dimerization as an autoregulatory mechanism for growth factor bioactivity and sets the stage for engineering modified FGF9 subfamily ligands, with desired activity for use in both basic and translational research.

  6. Preferential and rapid degradation of raw rice starch by an α-amylase of glycoside hydrolase subfamily GH13_37.

    Science.gov (United States)

    Lei, Yin; Peng, Hui; Wang, Ying; Liu, Yuantao; Han, Fang; Xiao, Yazhong; Gao, Yi

    2012-06-01

    The α-amylase (AmyP) from a marine metagenomic library belongs to the recently classified glycoside hydrolase subfamily GH13_37. The degradation abilities of AmyP on a broad range of raw starch granules were examined at 40 °C and pH 7.5. It was found that AmyP is a raw starch-degrading enzyme, exhibiting a unique and remarkable ability to preferentially and very rapidly digest raw rice starch. The specific activity of raw rice starch was reached 118.5 ± 0.6 Umg(-1), which was much higher than that of other raw starches. The final hydrolysis degrees were obtained in 4 h for 1 % raw rice starch and 1 h for 8 % concentration, indicating a very rapid speed of hydrolysis. The presence of a starch residue resistant was the main limiting factor for complete hydrolysis, although end product inhibition also existed, especially at high starch concentrations. AmyP randomly attacks unique or susceptible sites on raw rice starch granules, and releases glucose, maltose, and maltotriose as end products. This is the first biochemical characterization of the raw starch-degrading ability of an α-amylase of family GH13_37. The specific ability towards raw rice starch has never been described before, and this makes AmyP a promising candidate for use as a novel enzyme in rice starch processing.

  7. A novel DNMT3B subfamily, DeltaDNMT3B, is the predominant form of DNMT3B in non-small cell lung cancer.

    Science.gov (United States)

    Wang, Luo; Wang, Jie; Sun, Shiyong; Rodriguez, Marivonne; Yue, Ping; Jang, Se Jin; Mao, Li

    2006-07-01

    De novo promoter DNA methylation represses gene transcription and is a common mechanism to inactivate tumor suppressor genes in tumorigenesis. DNMT3B plays an important role in de novo DNA methylation. We report here the identification of a novel DNMT3B subfamily, termed DeltaDNMT3B, whose expression is initiated through a promoter located at intron 4 and exon 5 of the DNMT3B gene. At least 7 transcriptional variants of DeltaDNMT3B have been observed as the result of alternative pre-mRNA splicing. Predicted proteins derived from these variants suggest that 4 of the variants share a conservative enzymatic domain but contain a variable PWWP motif, a putative DNA binding structure, whereas 3 of the variants lack the enzymatic domain due to predicted premature translational termination. In non-small cell lung cancer (NSCLC) cell lines, DeltaDNMT3B variants are frequently expressed and are the predominant forms of DNMT3B. Similarly, DeltaDNMT3B variants are frequently expressed in primary NSCLC but are not detectable or are expressed at low levels in corresponding normal lung tissue. Our results indicate that DeltaDNMT3B is the major expression form of DNMT3B in NSCLC and may play an important role in the development of aberrant promoter methylation during lung tumorigenesis.

  8. Modulation of Kv3 subfamily potassium currents by the sea anemone toxin BDS: significance for CNS and biophysical studies.

    Science.gov (United States)

    Yeung, Shuk Yin M; Thompson, Dawn; Wang, Zhuren; Fedida, David; Robertson, Brian

    2005-09-21

    Kv3 potassium channels, with their ultra-rapid gating and high activation threshold, are essential for high-frequency firing in many CNS neurons. Significantly, the Kv3.4 subunit has been implicated in the major CNS disorders Parkinson's and Alzheimer's diseases, and it is claimed that selectively targeting this subunit will have therapeutic utility. Previous work suggested that BDS toxins ("blood depressing substance," from the sea anemone Anemonia sulcata) were specific blockers for rapidly inactivating Kv3.4 channels, and consequently these toxins are increasingly used as diagnostic agents for Kv3.4 subunits in central neurons. However, precisely how selective are these toxins for this important CNS protein? We show that BDS is not selective for Kv3.4 but markedly inhibits current through Kv3.1 and Kv3.2 channels. Inhibition comes about not by "pore block" but by striking modification of Kv3 gating kinetics and voltage dependence. Activation and inactivation kinetics are slowed by BDS-I and BDS-II, and V(1/2) for activation is shifted to more positive voltages. Alanine substitution mutagenesis around the S3b and S4 segments of Kv3.2 reveals that BDS acts via voltage-sensing domains, and, consistent with this, ON gating currents from nonconducting Kv3.2 are markedly inhibited. The altered kinetics and gating properties, combined with lack of subunit selectivity with Kv3 subunits, seriously affects the usefulness of BDS toxins in CNS studies. Furthermore, our results do not easily fit with the voltage sensor "paddle" structure proposed recently for Kv channels. Our data will be informative for experiments designed to dissect out the roles of Kv3 subunits in CNS function and dysfunction.

  9. The voltage-gated potassium channel subfamily KQT member 4 (KCNQ4) displays parallel evolution in echolocating bats.

    Science.gov (United States)

    Liu, Yang; Han, Naijian; Franchini, Lucía F; Xu, Huihui; Pisciottano, Francisco; Elgoyhen, Ana Belén; Rajan, Koilmani Emmanuvel; Zhang, Shuyi

    2012-05-01

    Bats are the only mammals that use highly developed laryngeal echolocation, a sensory mechanism based on the ability to emit laryngeal sounds and interpret the returning echoes to identify objects. Although this capability allows bats to orientate and hunt in complete darkness, endowing them with great survival advantages, the genetic bases underlying the evolution of bat echolocation are still largely unknown. Echolocation requires high-frequency hearing that in mammals is largely dependent on somatic electromotility of outer hair cells. Then, understanding the molecular evolution of outer hair cell genes might help to unravel the evolutionary history of echolocation. In this work, we analyzed the molecular evolution of two key outer hair cell genes: the voltage-gated potassium channel gene KCNQ4 and CHRNA10, the gene encoding the α10 nicotinic acetylcholine receptor subunit. We reconstructed the phylogeny of bats based on KCNQ4 and CHRNA10 protein and nucleotide sequences. A phylogenetic tree built using KCNQ4 amino acid sequences showed that two paraphyletic clades of laryngeal echolocating bats grouped together, with eight shared substitutions among particular lineages. In addition, our analyses indicated that two of these parallel substitutions, M388I and P406S, were probably fixed under positive selection and could have had a strong functional impact on KCNQ4. Moreover, our results indicated that KCNQ4 evolved under positive selection in the ancestral lineage leading to mammals, suggesting that this gene might have been important for the evolution of mammalian hearing. On the other hand, we found that CHRNA10, a gene that evolved adaptively in the mammalian lineage, was under strong purifying selection in bats. Thus, the CHRNA10 amino acid tree did not show echolocating bat monophyly and reproduced the bat species tree. These results suggest that only a subset of hearing genes could underlie the evolution of echolocation. The present work continues to

  10. A QUICK KEY TO THE SUBFAMILIES AND GENERA OF ANTS OF THE SAVANNAH RIVER SITE, AIKEN, SC

    Energy Technology Data Exchange (ETDEWEB)

    Martin, D

    2006-10-04

    This taxonomic key was devised to support development of a Rapid Bioassessment Protocol using ants at the Savannah River Site. The emphasis is on ''rapid'' and, because the available keys contained a large number of genera not known to occur at the Savannah River Site, we found that the available keys were unwieldy. Because these keys contained more genera than we would likely encounter and because this larger number of genera required both more couplets in the key and often required examination of characters that are difficult to assess without higher magnifications (60X or higher) more time was required to process samples. In developing this set of keys I recognize that the character sets used may lead to some errors but I believe that the error rate will be small and, for the purpose of rapid bioassessment, this error rate will be acceptable provided that overall sample sizes are adequate. Oliver and Beattie (1996a, 1996b) found that for rapid assessment of biodiversity the same results were found when identifications were done to morphospecies by people with minimal expertise as when the same data sets were identified by subject matter experts. Basset et al. (2004) concluded that it was not as important to correctly identify all species as it was to be sure that the study included as many functional groups as possible. If your study requires high levels of accuracy, it is highly recommended that when you key out a specimen and have any doubts concerning the identification, you should refer to keys in Bolton (1994) or to the other keys used to develop this area specific taxonomic key.

  11. A Functional Transcriptomic Approach to Understanding the Sand Fly Vector Relationships to the Host and Leshmania Parasites

    Science.gov (United States)

    2008-04-07

    Andersen J, Ribeiro JM: The invertebrate growth factor/CECR1 subfamily of adenosine deaminase proteins. Gene 2001, 267(1):13-22. 6. Cristalli G... Cristalli G, Costanzi S, Lambertucci C, Lupidi G, Vittori S, Volpini R, Camaioni E: Adenosine deaminase: functional implications and different

  12. A review of the Geocoridae of Mexico (Hemiptera: Heteroptera: Lygaeoidea), with descriptions of four new species, new distributional records, and a key to the known subfamilies, tribes, genera and species.

    Science.gov (United States)

    Brailovsky, Harry

    2016-10-06

    The family Geocoridae (Hemiptera: Heteroptera: Lygaeoidea) from Mexico is revised. Two subfamilies, one tribe, four genera, and fifteen species are treated in detail and descriptions or redescriptions are provided for all. Four new species of Geocoris are described: G. cervantesi (from Baja California), G. coahuilensis (from Coahuila), G. nuevoleonensis (from Nuevo Leon), and G. signoretae (from Aguascalientes, Hidalgo, and Puebla). The subspecies Geocoris thoracicus wickhami (Montandon) is considered a junior synonym of the nominal species G. thoracicus (Fieber). Key to subfamilies, tribes, genera and species recorded from Mexico are included. New distributional records for all of the previously known species are added. Isthmocoris slevini (Van Duzee) and I. tristis (Stål) are recorded for the first time from Mexico. Notes on the biology of most of the species are included. Color dorsal habitus photos, as well as drawings of the paramere, are included to aid in the identification of the species.

  13. Contributions to the knowledge of Formicidae (Hymenoptera, Aculeata: a new diagnosis of the family, the first global male-based key to subfamilies, and a treatment of early branching lineages

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    Brendon E. Boudinot

    2015-04-01

    Full Text Available The diagnosis of the Formicidae is revised, including five new, unreversed apomorphies, of which one is a unique synapomorphy. The first global male-based key to all subfamilies is provided and illustrated, and all ant subfamilies are diagnosed for males on a global scale for the first time. Three lineages of “basal ants” are assessed in detail: the Amblyoponinae, Leptanillinae, and Martialinae. The males of Martialis heureka (Martialinae and Apomyrma (Amblyoponinae are described. The Martialinae and Leptanillinae are diagnosed based on males, and additional diagnostic traits for the male of Amblyoponinae and worker of Martialis are provided. The placement of Scyphodon and Noonilla in the Formicidae and Leptanillinae is confirmed. Morphological characters of the Amblyoponinae, the Leptanillinae, and the Martialinae are contrasted, and potentially homologous apomorphies are signaled.

  14. Phylogenetic analysis of the spider mite sub-family Tetranychinae (Acari: Tetranychidae based on the mitochondrial COI gene and the 18S and the 5' end of the 28S rRNA genes indicates that several genera are polyphyletic.

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    Tomoko Matsuda

    Full Text Available The spider mite sub-family Tetranychinae includes many agricultural pests. The internal transcribed spacer (ITS region of nuclear ribosomal RNA genes and the cytochrome c oxidase subunit I (COI gene of mitochondrial DNA have been used for species identification and phylogenetic reconstruction within the sub-family Tetranychinae, although they have not always been successful. The 18S and 28S rRNA genes should be more suitable for resolving higher levels of phylogeny, such as tribes or genera of Tetranychinae because these genes evolve more slowly and are made up of conserved regions and divergent domains. Therefore, we used both the 18S (1,825-1,901 bp and 28S (the 5' end of 646-743 bp rRNA genes to infer phylogenetic relationships within the sub-family Tetranychinae with a focus on the tribe Tetranychini. Then, we compared the phylogenetic tree of the 18S and 28S genes with that of the mitochondrial COI gene (618 bp. As observed in previous studies, our phylogeny based on the COI gene was not resolved because of the low bootstrap values for most nodes of the tree. On the other hand, our phylogenetic tree of the 18S and 28S genes revealed several well-supported clades within the sub-family Tetranychinae. The 18S and 28S phylogenetic trees suggest that the tribes Bryobiini, Petrobiini and Eurytetranychini are monophyletic and that the tribe Tetranychini is polyphyletic. At the genus level, six genera for which more than two species were sampled appear to be monophyletic, while four genera (Oligonychus, Tetranychus, Schizotetranychus and Eotetranychus appear to be polyphyletic. The topology presented here does not fully agree with the current morphology-based taxonomy, so that the diagnostic morphological characters of Tetranychinae need to be reconsidered.

  15. Phylogenetic analysis of the spider mite sub-family Tetranychinae (Acari: Tetranychidae) based on the mitochondrial COI gene and the 18S and the 5' end of the 28S rRNA genes indicates that several genera are polyphyletic.

    Science.gov (United States)

    Matsuda, Tomoko; Morishita, Maiko; Hinomoto, Norihide; Gotoh, Tetsuo

    2014-01-01

    The spider mite sub-family Tetranychinae includes many agricultural pests. The internal transcribed spacer (ITS) region of nuclear ribosomal RNA genes and the cytochrome c oxidase subunit I (COI) gene of mitochondrial DNA have been used for species identification and phylogenetic reconstruction within the sub-family Tetranychinae, although they have not always been successful. The 18S and 28S rRNA genes should be more suitable for resolving higher levels of phylogeny, such as tribes or genera of Tetranychinae because these genes evolve more slowly and are made up of conserved regions and divergent domains. Therefore, we used both the 18S (1,825-1,901 bp) and 28S (the 5' end of 646-743 bp) rRNA genes to infer phylogenetic relationships within the sub-family Tetranychinae with a focus on the tribe Tetranychini. Then, we compared the phylogenetic tree of the 18S and 28S genes with that of the mitochondrial COI gene (618 bp). As observed in previous studies, our phylogeny based on the COI gene was not resolved because of the low bootstrap values for most nodes of the tree. On the other hand, our phylogenetic tree of the 18S and 28S genes revealed several well-supported clades within the sub-family Tetranychinae. The 18S and 28S phylogenetic trees suggest that the tribes Bryobiini, Petrobiini and Eurytetranychini are monophyletic and that the tribe Tetranychini is polyphyletic. At the genus level, six genera for which more than two species were sampled appear to be monophyletic, while four genera (Oligonychus, Tetranychus, Schizotetranychus and Eotetranychus) appear to be polyphyletic. The topology presented here does not fully agree with the current morphology-based taxonomy, so that the diagnostic morphological characters of Tetranychinae need to be reconsidered.

  16. Genetic association of aromatic hydrocarbon receptor (AHR) and cytochrome P450, family 1, subfamily A, polypeptide 1 (CYP1A1) polymorphisms with dioxin blood concentrations among pregnant Japanese women.

    Science.gov (United States)

    Kobayashi, Sumitaka; Sata, Fumihiro; Sasaki, Seiko; Ban, Susumu; Miyashita, Chihiro; Okada, Emiko; Limpar, Mariko; Yoshioka, Eiji; Kajiwara, Jumboku; Todaka, Takashi; Saijo, Yasuaki; Kishi, Reiko

    2013-06-07

    Dioxins are metabolized by cytochrome P450, family 1 (CYP1) via the aromatic hydrocarbon receptor (AHR). We determined whether different blood dioxin concentrations are associated with polymorphisms in AHR (dbSNP ID: rs2066853), AHR repressor (AHRR; rs2292596), CYP1 subfamily A polypeptide 1 (CYP1A1; rs4646903 and rs1048963), CYP1 subfamily A polypeptide 2 (CYP1A2; rs762551), and CYP1 subfamily B polypeptide 1 (CYP1B1; rs1056836) in pregnant Japanese women. These six polymorphisms were detected in 421 healthy pregnant Japanese women. Differences in dioxin exposure concentrations in maternal blood among the genotypes were investigated. Comparisons among the GG, GA, and AA genotypes of AHR showed a significant difference (genotype model: P=0.016 for the mono-ortho polychlorinated biphenyl concentrations and toxicity equivalence quantities [TEQs]). Second, we found a significant association with the dominant genotype model ([TT+TC] vs. CC: P=0.048 for the polychlorinated dibenzo-p-dioxin TEQs; P=0.035 for polychlorinated dibenzofuran TEQs) of CYP1A1 (rs4646903). No significant differences were found among blood dioxin concentrations and polymorphisms in AHRR, CYP1A1 (rs1048963), CYP1A2, and CYP1B1. Thus, polymorphisms in AHR and CYP1A1 (rs4646903) were associated with maternal dioxin concentrations. However, differences in blood dioxin concentrations were relatively low.

  17. Prognostic significance and molecular mechanism of ATP-binding cassette subfamily C member 4 in resistance to neoadjuvant radiotherapy of locally advanced rectal carcinoma.

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    Zhiqi Yu

    Full Text Available BACKGROUND: Mechanism of radioresistance in rectal carcinoma remains largely unknown. We aimed to evaluate the predictive role of ATP-binding cassette subfamily C member 4 (ABCC4 in locally advanced rectal carcinoma and explore possible molecular mechanisms by which ABCC4 confers the resistance to neoadjuvant radiotherapy. METHODS: The expression of ABCC4 and P53 mutant in biopsy tissue specimens from 121 locally advanced rectal carcinoma patients was examined using immunohistochemistry. The factors contributing to 3-year overall survival and disease-free survival were evaluated using the Kaplan-Meier method and Cox proportional hazard model. Lentivirus-mediated small hairpin RNA was applied to inhibit ABCC4 expression in colorectal carcinoma cell line RKO, and investigate the radiosensitivity in xenograft model. Intracellular cyclic adenosine monophosphate concentration and cell cycle distribution following irradiation were detected. RESULTS: High expression of ABCC4 and p53 mutant in pretreated tumors, poor pathological response, and high final tumor staging were significant factors independently predicted an unfavorable prognosis of locally advanced rectal carcinoma patients after neoadjuvant radiotherapy. Down-regulation of ABCC4 expression significantly enhanced irradiation-induced suppression of tumor growth in xenograft model. Furthermore, down-regulation of ABCC4 expression enhanced intracellular cyclic adenosine monophosphate production and noticeable deficiency of G1-S phase checkpoint in cell cycle following irradiation. CONCLUSIONS: Our study suggests that ABCC4 serves as a novel predictive biomarker that is responsible for the radioresistance and predicts a poor prognosis for locally advanced rectal carcinoma after neoadjuvant radiotherapy.

  18. Alona iheringula Sinev & Kotov, 2004 (Crustacea, Anomopoda, Chydoridae, Aloninae: life cycle and DNA barcode with implications for the taxonomy of the Aloninae subfamily.

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    Erika dos Santos Silva

    Full Text Available Knowledge of reproductive rates and life cycle of the Cladocera species is essential for population dynamic studies, secondary production and food webs, as well as the management and preservation of aquatic ecosystems. The present study aimed to understand the life cycle and growth of Alona iheringula Kotov & Sinev, 2004 (Crustacea, Anomopoda, Chydoridae, a Neotropical species, as well as its DNA barcoding, providing new information on the Aloninae taxonomy. The specimens were collected in the dammed portion of the Cabo Verde River (21°26'05″ S and 46°10'57″ W, in the Furnas Reservoir, Minas Gerais State, Brazil. Forty neonates were observed individually two or three times a day under controlled temperature (25±1°C, photoperiod (12 h light/12 h dark and feeding (Pseudokirchneriella subcapitata at a concentration of 105 cells.mL-1 and a mixed suspension of yeast and fish feed in equal proportion. Individual body growth was measured daily under optical microscope using a micrometric grid and 40× magnification. The species had a mean size of 413(±29 µm, a maximum size of 510 µm and reached maturity at 3.24(±0.69 days of age. Mean fecundity was 2 eggs per female per brood and the mean number of eggs produced per female during the entire life cycle was 47.6(±6.3 eggs per female. The embryonic development time was 1.79(±0.23 days and the maximum longevity was 54 days. The species had eight instars throughout its life cycle and four instars between neonate and primipara stage. The present study using molecular data (a 461 bp smaller COI fragment demonstrated a deep divergence in the Aloninae subfamily.

  19. Association with the Plasma Membrane Is Sufficient for Potentiating Catalytic Activity of Regulators of G Protein Signaling (RGS) Proteins of the R7 Subfamily.

    Science.gov (United States)

    Muntean, Brian S; Martemyanov, Kirill A

    2016-03-25

    Regulators of G protein Signaling (RGS) promote deactivation of heterotrimeric G proteins thus controlling the magnitude and kinetics of responses mediated by G protein-coupled receptors (GPCR). In the nervous system, RGS7 and RGS9-2 play essential role in vision, reward processing, and movement control. Both RGS7 and RGS9-2 belong to the R7 subfamily of RGS proteins that form macromolecular complexes with R7-binding protein (R7BP). R7BP targets RGS proteins to the plasma membrane and augments their GTPase-accelerating protein (GAP) activity, ultimately accelerating deactivation of G protein signaling. However, it remains unclear if R7BP serves exclusively as a membrane anchoring subunit or further modulates RGS proteins to increase their GAP activity. To directly answer this question, we utilized a rapidly reversible chemically induced protein dimerization system that enabled us to control RGS localization independent from R7BP in living cells. To monitor kinetics of Gα deactivation, we coupled this strategy with measuring changes in the GAP activity by bioluminescence resonance energy transfer-based assay in a cellular system containing μ-opioid receptor. This approach was used to correlate changes in RGS localization and activity in the presence or absence of R7BP. Strikingly, we observed that RGS activity is augmented by membrane recruitment, in an orientation independent manner with no additional contributions provided by R7BP. These findings argue that the association of R7 RGS proteins with the membrane environment provides a major direct contribution to modulation of their GAP activity.

  20. A REVISION OF THE PLIOCENE NATICIDS OF NORTHERN AND CENTRAL ITALY. II. THE SUBFAMILY NATICINAE: ADDITIONS TO COCHLIS, TANEA AND TECTONATICA

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    LUCA PEDRIALI

    2008-03-01

    Full Text Available The present paper is the second in a series devoted to the revision of the Pliocene naticids of Northern and Central Italy. It concludes the section covering the calcareous operculum-bearing Naticinae and expands to 18 the total number of species and subspecies of this subfamily recovered so far from the Pliocene deposits of Italy. Of the six taxa considered in this study, two (epigloafuniculata and fredianii fully match the characters of the genus Cochlis Röding, 1798, one (koeneni is assigned to the genus Tanea Marwick, 1931, the rest (astensis, prietoi and tectula belong to the genus Tectonatica Sacco, 1890. All the six taxa considered in this paper are described and commented in the systematic account. One, Cochlis fredianii, is proposed as new. In the chapter treating the generic assignment of the studied taxa, the range of Tanea, hitherto used to allocate several Indo-Pacific species, is extended to the Mediterranean Basin as well, and the relations between Tectonatica and Cryptonatica Dall, 1892 are discussed. This study further demonstrates that the morphological characters of the teleoconch are of low significance in species recognition. In fact, should the characters be ranked, the operculum comes first and is the primary element, sufficient to distinguish each species. The protoconch and the color pattern are the second and third relevant attributes that can be used diagnostically for several taxa, but not always. The other shell features appear to be useful tools in separating species only occasionally. Some species lack distinctive shell characters and do require operculate specimens in order to be confidently 

  1. Over-expression in Escherichia coli, purification and reconstitution in liposomes of the third member of the OCTN sub-family: The mouse carnitine transporter OCTN3

    Energy Technology Data Exchange (ETDEWEB)

    Scalise, Mariafrancesca; Galluccio, Michele; Pochini, Lorena [Department of Cell Biology, University of Calabria, Via P. Bucci 4c, 87036 Arcavacata di Rende (Italy); Indiveri, Cesare, E-mail: indiveri@unical.it [Department of Cell Biology, University of Calabria, Via P. Bucci 4c, 87036 Arcavacata di Rende (Italy)

    2012-05-25

    Highlights: Black-Right-Pointing-Pointer mOCTN3 transport protein has been cloned in pET-21a(+) and over-expressed in Escherichia coli. Black-Right-Pointing-Pointer The expressed mOCTN3 has been purified to homogeneity by Ni-chelating chromatography. Black-Right-Pointing-Pointer The protein solubilised in Triton X-100 has been reconstituted in liposomes. Black-Right-Pointing-Pointer Recombinant mOCTN3 catalyses transport of carnitine by a uniport mode. -- Abstract: pET-21a(+)-mOCTN3-6His was constructed and used for over-expression in Escherichia coli Rosetta(DE3)pLysS. After IPTG induction a protein with apparent molecular mass of 53 kDa was collected in the insoluble fraction of the cell lysate and purified by Ni{sup 2+}-chelating chromatography with a yield of 2 mg/l of cell culture. The over-expressed protein was identified with mOCTN3 by anti-His antibody and reconstitution in liposomes. mOCTN3 required peculiar conditions for optimal expression and reconstitution in liposomes. The protein catalyzed a time dependent [{sup 3}H]carnitine uptake which was stimulated by intraliposomal ATP and nearly independent of the pH. The K{sub m} for carnitine was 36 {mu}M. [{sup 3}H]carnitine transport was inhibited by carnitine analogues and some Cys and NH{sub 2} reagents. This paper represents the first outcome in over-expressing, in active form, the third member of the OCTN sub-family, mOCTN3, in E. coli.

  2. Nuclear receptor subfamily 2 group F member 1a (nr2f1a is required for vascular development in zebrafish.

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    Bao-Jueng Wu

    Full Text Available Genetic regulators and signaling pathways are important for the formation of blood vessels. Transcription factors controlling vein identity, intersegmental vessels (ISV growth and caudal vein plexus (CVP formation in zebrafish are little understood as yet. Here, we show the importance of the nuclear receptor subfamily member 1A (nr2f1a in zebrafish vascular development. Amino acid sequence alignment and phylogenetic analysis of nr2f1a is highly conserved among the vertebrates. Our in situ hybridization results showed nr2f1a mRNA is expressed in the lateral plate mesoderm at 18 somite stage and in vessels at 24-30 hpf, suggesting its roles in vasculization. Consistent with this morpholino-based knockdown of nr2fla impaired ISV growth and failed to develop fenestrated vascular structure in CVP, suggesting that nr2f1a has important roles in controlling ISV and CVP growth. Consequently, nr2f1a morphants showed pericardial edema and circulation defects. We further demonstrated reduced ISV cells and decreased CVP endothelial cells sprouting in nr2f1a morphants, indicating the growth impairment of ISV and CVP is due to a decrease of cell proliferation and migration, but not results from cell death in endothelial cells after morpholino knockdown. To test molecular mechanisms and signals that are associated with nr2f1a, we examined the expression of vascular markers. We found that a loss of nr2f1a results in a decreased expression of vein/ISV specific markers, flt4, mrc1, vascular markers stabilin and ephrinb2. This indicates the regulatory role of nr2f1a in controlling vascular development. We further showed that nr2f1a likely interact with Notch signaling by examining nr2f1a expression in rbpsuh morphants and DAPT-treatment embryos. Together, we show nr2f1a plays a critical role for vascular development in zebrafish.

  3. Venom peptide analysis of Vipera ammodytes meridionalis (Viperinae) and Bothrops jararacussu (Crotalinae) demonstrates subfamily-specificity of the peptidome in the family Viperidae.

    Science.gov (United States)

    Munawar, Aisha; Trusch, Maria; Georgieva, Dessislava; Spencer, Patrick; Frochaux, Violette; Harder, Sönke; Arni, Raghuvir K; Duhalov, Deyan; Genov, Nicolay; Schlüter, Hartmut; Betzel, Christian

    2011-12-01

    Snake venom peptidomes are valuable sources of pharmacologically active compounds. We analyzed the peptidic fractions (peptides with molecular masses Vipera ammodytes meridionalis (Viperinae), the most toxic snake in Europe, and Bothrops jararacussu (Crotalinae), an extremely poisonous snake of South America. Liquid chromatography/mass spectrometry (LC/MS), direct infusion electrospray mass spectrometry (ESI-MS) and matrix-assisted desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) were applied to characterize the peptides of both snake venoms. 32 bradykinin-potentiating peptides (BPPs) were identified in the Crotalinae venom and their sequences determined. 3 metalloproteinase inhibitors, 10 BPPs and a Kunitz-type inhibitor were observed in the Viperinae venom peptidome. Variability in the C-terminus of homologous BPPs was observed, which can influence the pharmacological effects. The data obtained so far show a subfamily specificity of the venom peptidome in the Viperidae family: BPPs are the major peptide component of the Crotalinae venom peptidome lacking Kunitz-type inhibitors (with one exception) while the Viperinae venom, in addition to BPPs, can contain peptides of the bovine pancreatic trypsin inhibitor family. We found indications for a post-translational phosphorylation of serine residues in Bothrops jararacussu venom BPP (S[combining low line]QGLPPGPPIP), which could be a regulatory mechanism in their interactions with ACE, and might influence the hypotensive effect. Homology between venom BPPs from Viperidae snakes and venom natriuretic peptide precursors from Elapidae snakes suggests a structural similarity between the respective peptides from the peptidomes of both snake families. The results demonstrate that the venoms of both snakes are rich sources of peptides influencing important physiological systems such as blood pressure regulation and hemostasis. The data can be used for pharmacological and medical applications.

  4. An approach to functionally relevant clustering of the protein universe: Active site profile-based clustering of protein structures and sequences.

    Science.gov (United States)

    Knutson, Stacy T; Westwood, Brian M; Leuthaeuser, Janelle B; Turner, Brandon E; Nguyendac, Don; Shea, Gabrielle; Kumar, Kiran; Hayden, Julia D; Harper, Angela F; Brown, Shoshana D; Morris, John H; Ferrin, Thomas E; Babbitt, Patricia C; Fetrow, Jacquelyn S

    2017-01-05

    Protein function identification remains a significant problem. Solving this problem at the molecular functional level would allow mechanistic determinant identification-amino acids that distinguish details between functional families within a superfamily. Active site profiling was developed to identify mechanistic determinants. DASP and DASP2 were developed as tools to search sequence databases using active site profiling. Here, TuLIP (Two-Level Iterative clustering Process) is introduced as an iterative, divisive clustering process that utilizes active site profiling to separate structurally characterized superfamily members into functionally relevant clusters. Underlying TuLIP is the observation that functionally relevant families (curated by Structure-Function Linkage Database, SFLD) self-identify in DASP2 searches; clusters containing multiple functional families do not. Each TuLIP iteration produces candidate clusters, each evaluated to determine if it self-identifies using DASP2. If so, it is deemed a functionally relevant group. Divisive clustering continues until each structure is either a functionally relevant group member or a singlet. TuLIP is validated on enolase and glutathione transferase structures, superfamilies well-curated by SFLD. Correlation is strong; small numbers of structures prevent statistically significant analysis. TuLIP-identified enolase clusters are used in DASP2 GenBank searches to identify sequences sharing functional site features. Analysis shows a true positive rate of 96%, false negative rate of 4%, and maximum false positive rate of 4%. F-measure and performance analysis on the enolase search results and comparison to GEMMA and SCI-PHY demonstrate that TuLIP avoids the over-division problem of these methods. Mechanistic determinants for enolase families are evaluated and shown to correlate well with literature results.

  5. Exact partition functions for gauge theories on Rλ3

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    Jean-Christophe Wallet

    2016-11-01

    Full Text Available The noncommutative space Rλ3, a deformation of R3, supports a 3-parameter family of gauge theory models with gauge-invariant harmonic term, stable vacuum and which are perturbatively finite to all orders. Properties of this family are discussed. The partition function factorizes as an infinite product of reduced partition functions, each one corresponding to the reduced gauge theory on one of the fuzzy spheres entering the decomposition of Rλ3. For a particular sub-family of gauge theories, each reduced partition function is exactly expressible as a ratio of determinants. A relation with integrable 2-D Toda lattice hierarchy is indicated.

  6. Exact partition functions for gauge theories on Rλ3

    Science.gov (United States)

    Wallet, Jean-Christophe

    2016-11-01

    The noncommutative space R,SUB>λ3, a deformation of R3, supports a 3-parameter family of gauge theory models with gauge-invariant harmonic term, stable vacuum and which are perturbatively finite to all orders. Properties of this family are discussed. The partition function factorizes as an infinite product of reduced partition functions, each one corresponding to the reduced gauge theory on one of the fuzzy spheres entering the decomposition of R&x03bb;3. For a particular sub-family of gauge theories, each reduced partition function is exactly expressible as a ratio of determinants. A relation with integrable 2-D Toda lattice hierarchy is indicated.

  7. A new species of Glaphyropoma: the first subterranean copionodontine catfish and the first occurrence of opercular odontodes in the subfamily (Siluriformes: Trichomycteridae

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    Maria Elina Bichuette

    2008-01-01

    Full Text Available A new species of the rare copionodontine genus Glaphyropoma is described from subterranean waters in the Diamantina Plateau, Bahia State, central northeastern Brazil. This is the first troglomorphic species in the subfamily Copionodontinae. It is distinguished from all other copionodontines by the presence of opercular odontodes, and further distinguished from its only congener, G. rodriguesi, by the reduction of dark integumentary pigmentation. The new species shares the single synapomorphy previously proposed for Glaphyropoma, the marked narrowing of the first hypobranchial and indirect character evidence also supports its inclusion in the genus. The presence of opercular odontodes in the new species, in combination with a reviewed hypothesis of sister group relationship between Copionodontinae and Trichogeninae, indicate that the absence of opercular odontodes in previously-known copionodontines is secondary, rather than primitive.Uma nova espécie do raro gênero de Copionodontinae Glaphyropoma é descrita de águas subterrâneas da Chapada Diamantina, estado da Bahia, região central do Nordeste Brasileiro. Esta é a primeira espécie troglomórfica na subfamília Copionodontinae. Distingue-se de todos os outros Copionodontinae pela presença de odontódeos operculares, e de seu único congênere, G. rodriguesi, também pela redução de pigmentação tegumentar. A nova espécie apresenta a única sinapomorfia previamente proposta para Glaphyropoma, um estreitamento acentuado do primeiro hipobranquial e evidência indireta de outros caracteres também suportam sua inclusão no gênero. A presença de odontódeos operculares na nova espécie, em combinação com uma hipótese revisada de grupo-irmão entre Copionodontinae e Trichogeninae, indica que a ausência de odontódeos operculares nos Copionodontinae previamente conhecidos é secundária e não primitiva.

  8. Amphibious Shelter-Builder Oniscidea Species from the New World with Description of a New Subfamily, a New Genus and a New Species from Brazilian Cave (Isopoda, Synocheta, Styloniscidae)

    Science.gov (United States)

    2015-01-01

    The new subfamily Iuiuniscinae, Styloniscidae, is erected for the new genus Iuiuniscus and the new species I. iuiuensis, which is described from cave of the State of Bahia, Northeastern Brazil. A special ecological character is shown here for the first time for a New World Oniscidea: the construction of mud shelters. An introduction addressing the systematics of Synocheta with emphasis on Styloniscidae Vandel, 1952 is provided, as well as general comments about the dependence of water in some Oniscidea and ecological traits of amphibious Synocheta. The problems referring to nomenclature, taxonomy and the interrelationships in Styloniscidae are discussed. PMID:25992909

  9. Amphibious shelter-builder Oniscidea species from the New World with description of a new subfamily, a new genus and a new species from Brazilian cave (Isopoda, Synocheta, Styloniscidae.

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    Leila A Souza

    Full Text Available The new subfamily Iuiuniscinae, Styloniscidae, is erected for the new genus Iuiuniscus and the new species I. iuiuensis, which is described from cave of the State of Bahia, Northeastern Brazil. A special ecological character is shown here for the first time for a New World Oniscidea: the construction of mud shelters. An introduction addressing the systematics of Synocheta with emphasis on Styloniscidae Vandel, 1952 is provided, as well as general comments about the dependence of water in some Oniscidea and ecological traits of amphibious Synocheta. The problems referring to nomenclature, taxonomy and the interrelationships in Styloniscidae are discussed.

  10. [Revision of of the subfamily of Metaracoelophryinae de Puytorac 1972 (Oligohymenophora: Hoplytophryida: Hoplytophryidae), astome ciliates of the digestive tract of Oligochaeta worms of Africa: description of five new species].

    Science.gov (United States)

    Fokam, Z; Ngassam, P; Nana, P A; Bricheux, G; Bouchard, P; Sime Ngando, T

    2012-02-01

    Five new species belonging to the astome ciliates, living in the digestive tract of Oligochaeta worms belonging to the genus Alma from Cameroon, have been described. The techniques used are: vital staining, staining of the nucleus with Diamidino Phenyl Indol (DAPI), scanning electron microscopy and silver staining method (Fernandez Galiano, 1976, 1994). This work confirms the presence of the genus Paracoelophrya and Dicoelophrya in the digestive track of the oligochaete Alma from Gabon and Cameroon; it helps to understand the general taxonomy of this Metaracoelophryinae subfamily. Moreover, the homogeneity of this group is confirmed and the phylogenetic relationship inside the Hoplitophryida order need more studies to be solved.

  11. Vector spaces on non-extendable holomorphic functions

    OpenAIRE

    Bernal-González, Luis

    2014-01-01

    In this paper, the linear structure of the family $H_e(G)$ of holomorphic functions in a domain $G$ of the complex plane that are not analytically continuable beyond the boundary of $G$ is analyzed. We prove that $H_e(G)$ contains, except for zero, a dense algebra; and, under appropriate conditions, the subfamily of $H_e(G)$ consisting of boundary-regular functions contains dense vector spaces with maximal dimension, as well as infinite dimensional closed vector spaces and large algebras. The...

  12. Systematics and phylogeny of the Neotropical treehopper subfamily Nicomiinae (Hemiptera, Membracidae Sistemática e filogenia das cigarrinhas neotropicais da subfamília Nicomiinae (Hemiptera, Membracidae

    Directory of Open Access Journals (Sweden)

    Jesse L. Albertson

    2005-03-01

    Full Text Available Morphological characters of adults of the treehopper subfamily Nicomiinae Haupt, 1929 (Hemiptera, Membracidae including seven genera (Eudonica gen. nov.; Euwalkeria Goding, 1926; Holdgatiella Evans, 1962; Nicomia Stål, 1858; Nodonica Dietrich, McKamey& Deitz, 2001; Stalomia gen. nov.; and Tolania Stål, 1858 and 22 species (16 new are described and illustrated. Keys are provided for genera and for species of Euwalkeria, Holdgatiella, and Nicomia. Nomenclatural changes, based on study of the primary type material of 15 species, include three new combinations, one new synonymy, and reinstatement of one junior synonym. Eudonica has one species, Eudonica nanella sp. nov.; Euwalkeria has five species, including four new species: E. colorata sp. nov., E. distincta sp. nov., E. perdita sp. nov., E. rubrica sp. nov.; Holdgatiella has two species, one of which is described as new: Holdgatiella chiloensis sp. nov.; Nicomia has twelve species, nine of which are described as new: N. buccina sp. nov., N. harenosa sp. nov., N. inscripta sp. nov., N. jucunda sp. nov., N. monticola sp. nov., N. nigrifasciata sp. nov., N. notidana sp. nov., N. pulchella sp. nov., N. serrata sp. nov.; Nodonica has one species, Nodonica bispinigera Dietrich, McKamey & Deitz; and Stalomia has one species, Stalomia veruta sp. nov. Tolania contains eleven previously described species and nearly 60 new species, which will be treated in a later publication. Three new combinations are proposed: one species described in Nicomia is placed in the tribe Abelini (Centrotinae as Abelus retrospinosus (Lethierry comb. nov.; one species previously placed in Nicomia is transferred to the genus Tolania as T. obliqua (Walker, 1858, comb. nov.; one species described in Holdgatiella is placed in the genus Tolania as T. stria (Cryan & Deitz, 2002, comb. nov. One new synonymy is proposed: Hoplophera [sic] cicadoides Walker, 1862, syn. nov., a junior synonym of Nicomia interrupta Stål, 1858. Nicomia

  13. Functional characterization of the TAS2R38 bitter taste receptor for phenylthiocarbamide in colobine monkeys.

    Science.gov (United States)

    Purba, Laurentia Henrieta Permita Sari; Widayati, Kanthi Arum; Tsutsui, Kei; Suzuki-Hashido, Nami; Hayakawa, Takashi; Nila, Sarah; Suryobroto, Bambang; Imai, Hiroo

    2017-01-01

    Bitterness perception in mammals is mostly directed at natural toxins that induce innate avoidance behaviours. Bitter taste is mediated by the G protein-coupled receptor TAS2R, which is located in taste cell membranes. One of the best-studied bitter taste receptors is TAS2R38, which recognizes phenylthiocarbamide (PTC). Here we investigate the sensitivities of TAS2R38 receptors to PTC in four species of leaf-eating monkeys (subfamily Colobinae). Compared with macaque monkeys (subfamily Cercopithecinae), colobines have lower sensitivities to PTC in behavioural and in vitro functional analyses. We identified four non-synonymous mutations in colobine TAS2R38 that are responsible for the decreased sensitivity of the TAS2R38 receptor to PTC observed in colobines compared with macaques. These results suggest that tolerance to bitterness in colobines evolved from an ancestor that was sensitive to bitterness as an adaptation to eating leaves. © 2017 The Author(s).

  14. Key to the subfamilies, tribes and genera of adult Dytiscidae of Argentina (Coleoptera: Adephaga Clave para los adultos de las subfamilias, tribus y géneros de Dytiscidae de la Argentina (Coleoptera: Adephaga

    Directory of Open Access Journals (Sweden)

    María L. Libonatti

    2011-12-01

    Full Text Available Dytiscids constitute the world's most speciose family of water beetles, whose identifi cation in Argentina is problematic with current keys. In this work, a key (both in English and Spanish to the eight subfamilies, 16 tribes and 31 genera of adult Dytiscidae of Argentina is presented. The key was constructed using stable qualitative characters of the external morphology and chaetotaxy, easily visualizable and interpretable. Characters such as size and shape of the body, color pattern and geographic distribution were also used. Illustrations of a great number of morphological structures as well as SEM micrographs were included to aid in the interpretation of the text. One subfamily (Hydrodytinae and fi ve genera (Agaporomorphus Zimmermann, Bidessodes Régimbart, Hydrodytes Miller, Queda Sharp and an unpublished genus of the subfamily Laccophilinae are cited for the fi rst time for Argentina.Los ditíscidos constituyen la familia más numerosa de escarabajos acuáticos a nivel mundial, cuya identifi cación en la Argentina resulta problemática con las claves actuales. En este trabajo, se presenta una clave (en inglés y español para los adultos de las ocho subfamilias, 16 tribus y 31 géneros de Dytiscidae de la Argentina. La clave fue construida priorizando la inclusión de caracteres cualitativos estables de la morfología externa y quetotaxia, fácilmente visibles e interpretables. También, se utilizaron caracteres como el tamaño y la forma del cuerpo, el patrón de coloración y la distribución geográfi ca. Se incluyeron ilustraciones de un gran número de estructuras morfológicas y fotografías tomadas con el microscopio electrónico, para ayudar a la interpretación del texto. Se citan, por primera vez para la Argentina, una subfamilia (Hydrodytinae y cinco géneros (Agaporomorphus Zimmermann, Bidessodes Régimbart, Hydrodytes Miller, Queda Sharp y un género inédito de la subfamilia Laccophilinae.

  15. A new genus and species of entocytherid ostracod (Ostracoda: Entocytheridae) from the John Day River Basin of Oregon, U.S.A., with a key to genera of the subfamily Entocytherinae.

    Science.gov (United States)

    Weaver, Patricia G; Williams, Bronwyn W

    2017-06-07

    Targeted sampling efforts by the authors for the signal crayfish, Pacifastacus leniusculus, from its native range in the John Day River Basin, Oregon, U.S.A. yielded entocytherid ostracods with a male copulatory complex so clearly different from other entocytherines that a new genus, Aurumcythere gen. nov. is proposed to receive them. This newly proposed, apparently nonsclerotized, genus with hook and spur-like prominences of the posteroventral end of the peniferum is the first new genus of the subfamily Entocytherinae named since Hobbs & Peters described Aphelocythere (= Waltoncythere) in 1977. Aurumcythere gen. nov. represents only the second genus of entocytherid known from the Pacific Northwest. Lack of sclerotization in Aurumcythere gen. nov. provides new insight into poorly understood mating behaviors of entocytherid ostracods.

  16. Updated keys to the genera in the subfamilies of Cyclocoelidae Stossich, 1902, including a reconsideration of species assignments, species keys and the proposal of a new genus in Szidatitreminae Dronen, 2007.

    Science.gov (United States)

    Dronen, Norman O; Blend, Charles K

    2015-12-08

    Keys to the six subfamilies, 22 genera within subfamilies and 128 species recognized within the Cyclocoelidae are provided. Lists of species in each genus are provided, along with taxonomic summaries that include type host, type locality, additional hosts, additional localities, previously proposed synonyms, and remarks for each species. The following synonymies are proposed: Cyclocoelum mutabile (Zeder, 1800)-Syn. C. microstomum (Creplin, 1929); Cyclocoelum leidyi Harrah, 1922-Syn. C. cuneatum Harrah, 1922; Cyclocoelum mehrotrai Sinha & Sahay, 1975-Syn. C. mathuri Jain, 1984; Selfcoelum allahabadi (Khan, 1935) n. comb.-Syns. Cyclocoelum agamprasadi Jain, 1983, Cyclocoelum erythropis Khan, 1935 and Cyclocoelum indicum Khan, 1935; Selfcoelum obliquum (Harrah, 1921) n. comb.-Syn. Cyclocoelum mehrii Khan, 1935; Uvitellina adelphus (Johnston, 1917)-Syn. Cyclocoelum (Uvitellina) dollfusi Tseng, 1930; Uvitellina kaniharensis (Gupta, 1958)-Syn. U. indica Siddiqi & Jairajpuri, 1962; Uvitellina simile (Stossich, 1902) n. comb.-Syn. U. magniembria Witenberg, 1923; Uvitellina vanelli (Rudolphi, 1819)-Syns. U. keri Yamaguti, 1933 and U. tageri Yamaguti, 1933; Wardianum triangulare (Harrah, 1922)-Syn. Wardianum catoptrophori Dronen, 2007; Haematotrephus limnodromi Dronen, Gardner & Jiménez, 2006-Syn. H. selfi Dronen, Gardner & Jiménez, 2008; and Hyptiasmus arcuatus (Brandes, 1892 of Stossich, 1902)-Syn. H. coelonodus Witenberg, 1923. Based on the lack of adequate descriptive information, Cyclocoelum cornu (Zeder, 1800); Cyclocoelum crenulatum (Rudolphi, 1809); Haematotrephus nigropunctatum (von Linstow, 1883) n. comb.; Haematotrephus robustus Ukoli, 1968; Hyptiasmus californicus (Wootton, 1966); and Hyptiasmus vigisi Savinov, 1960 are considered to be species inquirendae. Hyptiasmus witenbergi Tret'iakova, 1940 (described in a dissertation) is considered to be a nomen nudum. Comparative tables containing measurements, morphometric percentages and morphometric ratios for

  17. Rare mutations of FGFR2 causing Apert syndrome : identification of the first partial gene deletion, and an Alu element insertion from a new subfamily

    NARCIS (Netherlands)

    Bochukova, E.G.; Roscioli, T.; Hedges, D.J.; Taylor, I.B.; Johnson, D.; David, D.J.; Deininger, P.L.; Wilkie, A.O.

    2009-01-01

    Apert syndrome (AS) is a severe disorder, characterized by craniosynostosis and complex syndactyly of the hands and feet. Two heterozygous gain-of-function substitutions (Ser252Trp and Pro253Arg) in exon IIIa of fibroblast growth factor receptor 2 (FGFR2) are responsible for >98% of cases. Here we d

  18. The terpene synthase gene family in Tripterygium wilfordii harbors a labdane-type diterpene synthase among the monoterpene synthase TPS-b subfamily

    DEFF Research Database (Denmark)

    Hansen, Nikolaj L; Heskes, Allison M; Hamberger, Britta;

    2017-01-01

    in the formation of four C-20 diphosphate intermediates, precursors of both generalized and specialized metabolism and a novel scaffold for Celastraceae. Functional pairs of the class I and II enzymes resulted in formation of three scaffolds, accounting for some of the terpenoid diversity found in T. wilfordii...

  19. Genome-wide expression analysis of soybean MADS genes showing potential function in the seed development.

    Directory of Open Access Journals (Sweden)

    Cheng-Ming Fan

    Full Text Available The MADS family is an ancient and best-studied transcription factor and plays fundamental roles in almost every developmental process in plants. In the plant evolutionary history, the whole genome duplication (WGD events are important not only to the plant species evolution, but to expansion of members of the gene families. Soybean as a model legume crop has experience three rounds of WGD events. Members of some MIKC(C subfamilies, such as SOC, AGL6, SQUA, SVP, AGL17 and DEF/GLO, were expanded after soybean three rounds of WGD events. And some MIKC(C subfamilies, MIKC* and type I MADS families had experienced faster birth-and-death evolution and their traces before the Glycine WGD event were not found. Transposed duplication played important roles in tandem arrangements among the members of different subfamilies. According to the expression profiles of type I and MIKC paralog pair genes, the fates of MIKC paralog gene pairs were subfunctionalization, and the fates of type I MADS paralog gene pairs were nonfunctionalization. 137 out of 163 MADS genes were close to 186 loci within 2 Mb genomic regions associated with seed-relative QTLs, among which 115 genes expressed during the seed development. Although MIKC(C genes kept the important and conserved functions of the flower development, most MIKC(C genes showed potentially essential roles in the seed development as well as the type I MADS.

  20. New sub-family of lysozyme-like proteins shows no catalytic activity: crystallographic and biochemical study of STM3605 protein from Salmonella Typhimurium

    Energy Technology Data Exchange (ETDEWEB)

    Michalska, Karolina; Brown, Roslyn N.; Li, Hui; Jedrzejczak, Robert; Niemann, George; Heffron, Fred; Cort, John R.; Adkins, Joshua N.; Babnigg, Gyorgy; Joachimiak, Andrzej

    2013-03-01

    Phage viruses that infect prokaryotes integrate their genome into the host chromosome; thus, microbial genomes typically contain genetic remnants of both recent and ancient phage infections. Often phage genes occur in clusters of atypical G+C content that reflect integration of the foreign DNA. However, some phage genes occur in isolation without other phage gene neighbors, probably resulting from horizontal gene transfer. In these cases, the phage gene product is unlikely to function as a component of a mature phage particle, and instead may have been co-opted by the host for its own benefit. The product of one such gene from Salmonella enterica serovar Typhimurium, STM3605, encodes a protein with modest sequence similarity to phage-like lysozyme (N-acetylmuramidase) but appears to lack essential catalytic residues that are strictly conserved in all lysozymes. Close homologs in other bacteria share this characteristic. The structure of the STM3605 protein was characterized by X-ray crystallography, and functional assays showed that it is a stable, folded protein whose structure closely resembles lysozyme. However, this protein is unlikely to hydrolyze peptidoglycan. Instead, STM3605 is presumed to have evolved an alternative function because it shows some lytic activity and partitions to micelles.

  1. Revision of the Oriental subfamily Heteropteryginae Kirby, 1896, with a re-arrangement of the family Heteropterygidae and the descriptions of five new species of Haaniella Kirby, 1904. (Phasmatodea: Areolatae: Heteropterygidae).

    Science.gov (United States)

    Hennemann, Frank H; Conle, Oskar V; Brock, Paul D; Seow-Choen, Francis

    2016-09-01

    The areolate Oriental family Heteropterygidae Kirby, 1893 is critically reviewed and the results of the present study contradict the arrangement suggested by Zompro (2004), but in most aspects agree with a molecular study presented by Whiting et al (2003) and a phylogenetic study presented by Bradler (2009). The family is critically discussed and new hypotheses are presented for the phylogeny and intra-familiar relationships, placing the subfamily Dataminae Rehn & Rehn, 1939 as the basalmost clade of Heteropterygidae. The subfamilies Obriminae Brunner v. Wattenwyl, 1893 and Heteropteryginae Kirby, 1893 together represent the sister-group of Dataminae. Arguments and a tree are presented to support this hypothesis. New diagnoses and lists of genera are provided for all three subfamilies contained in Heteropterygidae, along with keys to distinguish between them.        The subfamily Obriminae is critically reviewed and the distinction between the three tribes Obrimini Brunner v. Wattenwyl, 1893, Eubulidini Zompro, 2004 and Miroceramiini Zompro, 2004 introduced by Zompro (2004) is shown to be poorly supported. While Obrimini sensu Zompro, 2004 is generally accepted (but now also contains genera that were placed in Eubulidini or Miroceramiini by Zompro (2004)), the tribes Eubulidini and Miroceramiini are not supported. A new arrangement is introduced, which is based on morphological characters neglected or overlooked by Zompro (2004) but were partly discussed by Bradler (2009). The genus Mearnsiana Rehn & Rehn, 1939 is removed from Miroceramiini and transferred to Obrimini. The genera Eubulides Stål, 1877, Heterocopus Redtenbacher, 1906, Theramenes Stål, 1875 and Stenobrimus Redtenbacher, 1906 are removed from Eubulidini and also transferred to Obrimini. Consequently, Eubulidini is synonymised with Obrimini (n. syn.). Miroceramiini is a monotypical tribe and only includes the Wallacean genus Miroceramia Günther, 1934. The new tribe Tisamenini n. trib. is

  2. Checklist of Chinese Ants :Formicomorph Subfamilies (Hymenoptera : Formicidae) (Ⅱ)%中国蚁科昆虫名录——蚁型亚科群(膜翅目:蚁科)(Ⅱ)

    Institute of Scientific and Technical Information of China (English)

    冉浩; 周善义

    2012-01-01

    本文总结中国蚁型亚科群(the formicomorph subfamilies)蚁亚科Formieinae已知昆虫10属107种4亚种,其中箭蚁属Cataglyphis 7种,蚁属Formica 44种1亚种,短角蚁属Gesomyrmex 1种,毛蚁属Lasius 19种,刺结蚁属Lepisiota 8种3亚种,长齿蚁属Myrmoteras 2种,尼氏蚁属Nylanderia 21种,织叶蚁属Oecophylla 1种,拟立毛蚁属Paraparatrechina 3种,立毛蚁属Paratrechina 1种.因长有德和贺达汉于2002年命名的粗壮黑蚁的Formica robusta已被Carpenter占用,故将其重命名为长贺氏蚁Formica changhei Ran et Zhou.根据Lapolla最新研究成果,将观音立毛蚁和孔明立毛蚁从立毛蚁属Paratrechina中移至拟立毛蚁属Paraparatrechina,提出了2个新组合,即:观音拟立毛蚁Paraparatrechina guanyin (Terayama,2009)com.nov.和孔明拟立毛蚁Paraparatrechina kongming (Terayama,2009) com.nov..文中给出各种的中文译名、拉丁学名和分布,并对近年来分类地位发生变化、具有较大经济意义和社会意义的种,以及需要特别说明的种作了注解.%107 known species, 4 subspcies belonging to 10 genera of the subfamily Formicinae of the formicomorph subfamilies from China are listed. Among them Cataglyphis with 7 species, Formica with 44 species and 1 subspecies,Gesomyrmex with 1 species,Lasius with 19 species,Lepisiota with 8 species and 3 subspecies,Myrmoteras with 2 species,Nylanderia with 21 species,Oecophylla with 1 species,Para-paratrechina with 3 species,and Paratrechina with 1 species. Formica robusta Chang et He,2002 was renamed as Formica changhei Ran et Zhou as the former was occupied by Formica robusta Carpenter. According to the results of Lapolla et al. ,removed guanyin and kongming from the genus Paratrechina to the genus Paraparatrechina, and combinated two species, i. e. Paraparatrechina guanyin (Terayama, 2009),com. nov. and Paraparatrechina kongming (Terayama,2009) ,com. nov.. All species were treated with Chinese translated names and latin names

  3. Expansion and Functional Divergence of Jumonji C-Containing Histone Demethylases: Significance of Duplications in Ancestral Angiosperms and Vertebrates.

    Science.gov (United States)

    Qian, Shengzhan; Wang, Yingxiang; Ma, Hong; Zhang, Liangsheng

    2015-08-01

    Histone modifications, such as methylation and demethylation, are crucial mechanisms altering chromatin structure and gene expression. Recent biochemical and molecular studies have uncovered a group of histone demethylases called Jumonji C (JmjC) domain proteins. However, their evolutionary history and patterns have not been examined systematically. Here, we report extensive analyses of eukaryotic JmjC genes and define 14 subfamilies, including the Lysine-Specific Demethylase3 (KDM3), KDM5, JMJD6, Putative-Lysine-Specific Demethylase11 (PKDM11), and PKDM13 subfamilies, shared by plants, animals, and fungi. Other subfamilies are detected in plants and animals but not in fungi (PKDM12) or in animals and fungi but not in plants (KDM2 and KDM4). PKDM7, PKDM8, and PKDM9 are plant-specific groups, whereas Jumonji, AT-Rich Interactive Domain2, KDM6, and PKDM10 are animal specific. In addition to known domains, most subfamilies have characteristic conserved amino acid motifs. Whole-genome duplication (WGD) was likely an important mechanism for JmjC duplications, with four pairs from an angiosperm-wide WGD and others from subsequent WGDs. Vertebrates also experienced JmjC duplications associated with the vertebrate ancestral WGDs, with additional mammalian paralogs from tandem duplication and possible transposition. The sequences of paralogs have diverged in both known functional domains and other regions, showing evidence of selection pressure. The increases of JmjC copy number and the divergences in sequence and expression might have contributed to the divergent functions of JmjC genes, allowing the angiosperms and vertebrates to adapt to a great number of ecological niches and contributing to their evolutionary successes.

  4. Characterization of a pituitary-tumor-derived cell line, TtT/GF, that expresses Hoechst efflux ABC transporter subfamily G2 and stem cell antigen 1.

    Science.gov (United States)

    Mitsuishi, Hideo; Kato, Takako; Chen, Mo; Cai, Li-Yi; Yako, Hideji; Higuchi, Masashi; Yoshida, Saishu; Kanno, Naoko; Ueharu, Hiroki; Kato, Yukio

    2013-11-01

    The anterior lobe of the pituitary gland is composed of five types of endocrine cells and of non-endocrine folliculo-stellate cells that produce various local signaling molecules. The TtT/GF cell line is derived from pituitary tumors, produces no hormones and has folliculo-stellate cell-like characteristics. The biological function of TtT/GF cells remains elusive but several properties have been postulated (support of endocrine cells, control of cell proliferation, scavenger function). Recently, we observed that TtT/GF cells have high resistance to the antibiotic G418 and low influx for Hoechst 33342, indicating the presence of ATP-binding cassette (ABC) transporters that efflux multiple drugs, i.e., a property similar to that of stem/progenitor cells. Therefore, we examine TtT/GF cells for the presence of ABC transporters, for the efflux ability of Hoechst 33342 and for those genes characteristic of TtT/GF cells. Real-time polymerase chain reaction (PCR) for ABC transporters demonstrated that Abcb1a, Abcb1b and Abcg2, regarded as stem cell markers, were characteristically expressed in TtT/GF cells but not in Tpit/F1 and LβT2 cells. Furthermore, the remarkable low-efflux ability of Hoechst 33342 from TtT/GF cells was confirmed by using inhibitors and contrasted with the abilities of Tpit/F1 and LβT2 cells. The high and specific expression of stem cell antigen 1 (Sca1) in TtT/GF cells was confirmed by real-time PCR. We also demonstrated those genes that are expressed abundantly and characteristically in TtT/GF, suggesting that TtT/GF cells have unique characteristics similar to those of stem/progenitor cells of endothelial or mesenchymal origin. Thus, the present study has revealed an intriguing property of TtT/GF cells, providing a new clue for an understanding of the function of this cell line.

  5. The Roles of Orphan Nuclear Receptors in the Development and Function of the Immune System

    Institute of Scientific and Technical Information of China (English)

    Ivan Dzhagalov; Nu Zhang; You-Wen He

    2004-01-01

    Hormones and their receptors regulate cell growth, differentiation and apoptosis and also play important roles in immune function. Recent studies on the subfamily of the orphan nuclear receptors known as retinoid-acid related orphan receptors (ROR) have shed important insights on the roles of this group of nuclear proteins in the development and function of the immune system. RORα regulates inflammatory cytokine production in both innate and adaptive immune system while RORγ regulates the normal development of T lymphocyte repertoire and secondary lymphoid organs. Cellular & Molecular Immunology. 2004;1(6):401-407.

  6. The Roles of Orphan Nuclear Receptors in the Development and Function of the Immune System

    Institute of Scientific and Technical Information of China (English)

    IvanDzhagalov; NuZhang; You-WenHe

    2004-01-01

    Hormones and their receptors regulate cell growth, differentiation and apoptosis and also play important roles in immune function. Recent studies on the subfamily of the orphan nuclear receptors known as retinoid-acid related orphan receptors (ROR) have shed important insights on the roles of this group of nuclear proteins in the development and function of the immune system. RORα regulates inflammatory cytokine production in both innate and adaptive immune system while RORγ, regulates the normal development of T lymphocyte repertoire and secondary lymphoid organs. Cellular & Molecular Immunology. 2004;1(6):401-407.

  7. Positive selection pressure within teleost Toll-like receptors tlr21 and tlr22 subfamilies and their response to temperature stress and microbial components in zebrafish.

    Science.gov (United States)

    Sundaram, Arvind Y M; Consuegra, Sonia; Kiron, Viswanath; Fernandes, Jorge M O

    2012-09-01

    Toll-like receptors (TLRs) play a crucial role in host defence, since they trigger immune response following recognition of pathogen-associated molecular patterns (PAMPs) in potential infectious agents. TLRs have been found in numerous organisms, including mammals, birds and teleosts. Some TLR members are commonly retained across all species, whilst others were lost, gained or diverged independently during evolution. Our knowledge about the evolution and specific functions of tlr21, tlr22 and tlr23 in teleosts are still scarce. Phylogenetic analysis of 18 tlr13, tlr21, tlr22 and tlr23 genes from 9 different fish species divided them in two groups. All tlr21 genes were under the first clade, while the second comprised tlr22, tlr23 and tlr13 from Atlantic salmon. Evidence of positive selection was detected at three sites within the leucine-rich repeat regions of Tlr22, which may influence PAMP recognition. Immunostimulation experiments revealed that expression of zebrafish tlr22 is modulated by several unrelated PAMPs. Up to a 3-fold increase in tlr21 and tlr22 expression was detected in larvae exposed to immunostimulants such as lipopolysaccharide, peptidoglycan or poly I:C. We found that zebrafish tlrs are expressed mainly in immune-related organs, such as spleen and kidney as well as in testis and temperature stress did not have an effect on the expression of tlr21 and tlr22 in the early stages of development in zebrafish larvae. Our data indicates that these teleost tlrs may play a role in innate host defence. In particular, tlr22 is evolving under positive selection, which indicates functional diversification and adaptation of the response to different PAMPs.

  8. VirS, an OmpR/PhoB subfamily response regulator, is required for activation of vapA gene expression in Rhodococcus equi.

    Science.gov (United States)

    Kakuda, Tsutomu; Hirota, Takuya; Takeuchi, Tatsuya; Hagiuda, Hirofumi; Miyazaki, Shiko; Takai, Shinji

    2014-10-03

    Rhodococcus equi is an important pulmonary pathogen in foals and in immunocompromised individuals. Virulent R. equi strains carry an 80-90 kb virulence plasmid that expresses the virulence-associated protein A (VapA). VapA expression is regulated by temperature and pH. The LysR-type transcriptional regulator, VirR, is involved in the regulation of the vapA gene. To examine the mechanism underlying transcriptional regulation of vapA, we characterized an R. equi mutant in which another putative transcriptional regulator encoded on the virulence plasmid, VirS, was deleted. Deletion of virS reduced vapA promoter activity to non-inducible levels. Complementary expression of VirS in the virS deletion mutant restored transcription at the PvapA promoter, even under non-inducing conditions (30°C and pH 8.0). In addition, VirS expression increased PvapA promoter activity in the absence of functional VirR. Further, transcription of the icgA operon containing virS was regulated by pH and temperature in the same manner as vapA. This study suggests that VirS is required for VapA expression and that regulation of PvapA-promoter activity may be achieved by controlling VirS expression levels.

  9. In Silico/In Vivo Insights into the Functional and Evolutionary Pathway of Pseudomonas aeruginosa Oleate-Diol Synthase. Discovery of a New Bacterial Di-Heme Cytochrome C Peroxidase Subfamily

    OpenAIRE

    Mónica Estupiñán; Daniel Álvarez-García; Xavier Barril; Pilar Diaz; Angeles Manresa

    2015-01-01

    As previously reported, P. aeruginosa genes PA2077 and PA2078 code for 10S-DOX (10S-Dioxygenase) and 7,10-DS (7,10-Diol Synthase) enzymes involved in long-chain fatty acid oxygenation through the recently described oleate-diol synthase pathway. Analysis of the amino acid sequence of both enzymes revealed the presence of two heme-binding motifs (CXXCH) on each protein. Phylogenetic analysis showed the relation of both proteins to bacterial di-heme cytochrome c peroxidases (Ccps), similar to Xa...

  10. 中国细蚁亚科系统分类研究(膜翅目:蚁科)%A Systematic Study on the Ant Subfamily Leptanillinae of China ( Hymenoptera: Formicidae)

    Institute of Scientific and Technical Information of China (English)

    徐正会

    2002-01-01

    Two genera of the ant subfamily Leptanillinae are recorded in China. Three species including a new species of the genus LeptanillaEmery are reported: L. hunaneasis Tang, Li et Chen from Hunan Province, L. taiwanensis Ogata, Terayama et Masuko from Taiwan Province, L. yuananensis sp. nov. from Yunnan Province. Protanilla Taylor is newly recorded in China, of which 2 new species are describedfrom Yunnan Province, i.e.P, concolor sp. nov. and P. bicolor sp. nov. Keys to the two genera of Leptanillinae and their species in Chinabased on worker caste are provided%记载中国细蚁亚科kptanilliBae昆虫2属.报道细蚁属Leptanilla Emery3种:湖南细蚁L. hunanensis Tang, Li et Chen 分布于湖南省,台湾细蚁L. taiwanensis Ogata, Terayama et Masuko分布于台湾省,云南细蚁L. yunnanensis sp. nov.分布于云南省.原细蚁属Protanilla Taylor为中国新记录属,在云南省采集并描述该属2新种:单色原细蚁P. concolor sp. nov.和双色原细蚁P.bicolor sp.nov..编制了细蚁亚科这2属的工蚁分属检索表和中国分布种工蚁分种检索表.

  11. Identification and characterization of CbeI, a novel thermostable restriction enzyme from Caldicellulosiruptor bescii DSM 6725 and a member of a new subfamily of HaeIII-like enzymes.

    Science.gov (United States)

    Chung, Dae-Hwan; Huddleston, Jennifer R; Farkas, Joel; Westpheling, Janet

    2011-11-01

    Potent HaeIII-like DNA restriction activity was detected in cell-free extracts of Caldicellulosiruptor bescii DSM 6725 using plasmid DNA isolated from Escherichia coli as substrate. Incubation of the plasmid DNA in vitro with HaeIII methyltransferase protected it from cleavage by HaeIII nuclease as well as cell-free extracts of C. bescii. The gene encoding the putative restriction enzyme was cloned and expressed in E. coli with a His-tag at the C-terminus. The purified protein was 38 kDa as predicted by the 981-bp nucleic acid sequence, was optimally active at temperatures between 75°C and 85°C, and was stable for more than 1 week when stored at 35°C. The cleavage sequence was determined to be 5'-GG/CC-3', indicating that CbeI is an isoschizomer of HaeIII. A search of the C. bescii genome sequence revealed the presence of both a HaeIII-like restriction endonuclease (Athe 2438) and DNA methyltransferase (Athe 2437). Preliminary analysis of other Caldicellulosiruptor species suggested that this restriction/modification activity is widespread in this genus. A phylogenetic analysis based on sequence alignment and conserved motif searches identified features of CbeI distinct from other members of this group and classified CbeI as a member of a novel subfamily of HaeIII-like enzymes.

  12. Functions of Polo-Like Kinases: A Journey From Yeast To Humans.

    Science.gov (United States)

    Vaid, Rajni; Sharma, Nitin; Chauhan, Sujata; Deshta, Ankita; Dev, Kamal; Sourirajan, Anuradha

    2016-01-01

    Polo-like kinases (PLKs) belong to the serine/threonine kinase subfamily, characterized by the presence of the signature motif called Polo-box domain. PLK members studied so far have emerged as the conserved regulator of cell cycle and cell division in eukaryotes. The Polo-box domain adds diversity to PLK functions by targeting the enzyme to an array of substrates found at different sub-cellular structures for exquisite regulation of cell cycle. More than a dozen members of PLK subfamily have been identified in the eukaryotic world except in the higher plants. Despite the similarities in governing cell division, PLKs have diverse and unique functions in different organisms. This review summarizes the plethora of functions of PLK in yeast to humans. Along with its classical functions, this review also emphasizes on the role of PLKs in regulating DNA replication, repair, genome integrity, development, and morphogenesis pathways. Perturbations in PLK functions have disease implications, such as cancer in humans, and thus human PLK1 is targeted for cancer therapeutics. PLKs also play a vital role in regulating several stages of meiotic cell division. Thus, PLKs are emerging as a unique class of proteins with multiple and diverse functions in different organisms.

  13. Structure of Human B12 Trafficking Protein CblD Reveals Molecular Mimicry and Identifies a New Subfamily of Nitro-FMN Reductases*

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    Yamada, Kazuhiro; Gherasim, Carmen; Banerjee, Ruma; Koutmos, Markos

    2015-01-01

    In mammals, B12 (or cobalamin) is an essential cofactor required by methionine synthase and methylmalonyl-CoA mutase. A complex intracellular pathway supports the assimilation of cobalamin into its active cofactor forms and delivery to its target enzymes. MMADHC (the methylmalonic aciduria and homocystinuria type D protein), commonly referred to as CblD, is a key chaperone involved in intracellular cobalamin trafficking, and mutations in CblD cause methylmalonic aciduria and/or homocystinuria. Herein, we report the first crystal structure of the globular C-terminal domain of human CblD, which is sufficient for its interaction with MMADHC (the methylmalonic aciduria and homocystinuria type C protein), or CblC, and for supporting the cytoplasmic cobalamin trafficking pathway. CblD contains an α+β fold that is structurally reminiscent of the nitro-FMN reductase superfamily. Two of the closest structural relatives of CblD are CblC, a multifunctional enzyme important for cobalamin trafficking, and the activation domain of methionine synthase. CblD, CblC, and the activation domain of methionine synthase share several distinguishing features and, together with two recently described corrinoid-dependent reductive dehalogenases, constitute a new subclass within the nitro-FMN reductase superfamily. We demonstrate that CblD enhances oxidation of cob(II)alamin bound to CblC and that disease-causing mutations in CblD impair the kinetics of this reaction. The striking structural similarity of CblD to CblC, believed to be contiguous in the cobalamin trafficking pathway, suggests the co-option of molecular mimicry as a strategy for achieving its function. PMID:26364851

  14. Structure of Human B12 Trafficking Protein CblD Reveals Molecular Mimicry and Identifies a New Subfamily of Nitro-FMN Reductases.

    Science.gov (United States)

    Yamada, Kazuhiro; Gherasim, Carmen; Banerjee, Ruma; Koutmos, Markos

    2015-12-04

    In mammals, B12 (or cobalamin) is an essential cofactor required by methionine synthase and methylmalonyl-CoA mutase. A complex intracellular pathway supports the assimilation of cobalamin into its active cofactor forms and delivery to its target enzymes. MMADHC (the methylmalonic aciduria and homocystinuria type D protein), commonly referred to as CblD, is a key chaperone involved in intracellular cobalamin trafficking, and mutations in CblD cause methylmalonic aciduria and/or homocystinuria. Herein, we report the first crystal structure of the globular C-terminal domain of human CblD, which is sufficient for its interaction with MMADHC (the methylmalonic aciduria and homocystinuria type C protein), or CblC, and for supporting the cytoplasmic cobalamin trafficking pathway. CblD contains an α+β fold that is structurally reminiscent of the nitro-FMN reductase superfamily. Two of the closest structural relatives of CblD are CblC, a multifunctional enzyme important for cobalamin trafficking, and the activation domain of methionine synthase. CblD, CblC, and the activation domain of methionine synthase share several distinguishing features and, together with two recently described corrinoid-dependent reductive dehalogenases, constitute a new subclass within the nitro-FMN reductase superfamily. We demonstrate that CblD enhances oxidation of cob(II)alamin bound to CblC and that disease-causing mutations in CblD impair the kinetics of this reaction. The striking structural similarity of CblD to CblC, believed to be contiguous in the cobalamin trafficking pathway, suggests the co-option of molecular mimicry as a strategy for achieving its function.

  15. Expanded functional diversity of shaker K(+ channels in cnidarians is driven by gene expansion.

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    Timothy Jegla

    Full Text Available The genome of the cnidarian Nematostella vectensis (starlet sea anemone provides a molecular genetic view into the first nervous systems, which appeared in a late common ancestor of cnidarians and bilaterians. Nematostella has a surprisingly large and diverse set of neuronal signaling genes including paralogs of most neuronal signaling molecules found in higher metazoans. Several ion channel gene families are highly expanded in the sea anemone, including three subfamilies of the Shaker K(+ channel gene family: Shaker (Kv1, Shaw (Kv3 and Shal (Kv4. In order to better understand the physiological significance of these voltage-gated K(+ channel expansions, we analyzed the function of 18 members of the 20 gene Shaker subfamily in Nematostella. Six of the Nematostella Shaker genes express functional homotetrameric K(+ channels in vitro. These include functional orthologs of bilaterian Shakers and channels with an unusually high threshold for voltage activation. We identified 11 Nematostella Shaker genes with a distinct "silent" or "regulatory" phenotype; these encode subunits that function only in heteromeric channels and serve to further diversify Nematostella Shaker channel gating properties. Subunits with the regulatory phenotype have not previously been found in the Shaker subfamily, but have evolved independently in the Shab (Kv2 family in vertebrates and the Shal family in a cnidarian. Phylogenetic analysis indicates that regulatory subunits were present in ancestral cnidarians, but have continued to diversity at a high rate after the split between anthozoans and hydrozoans. Comparison of Shaker family gene complements from diverse metazoan species reveals frequent, large scale duplication has produced highly unique sets of Shaker channels in the major metazoan lineages.

  16. Structural and functional significance of the FGL sequence of the periplasmic chaperone Caf1M of Yersinia pestis.

    Science.gov (United States)

    Chapman, D A; Zavialov, A V; Chernovskaya, T V; Karlyshev, A V; Zav'yalova, G A; Vasiliev, A M; Dudich, I V; Abramov, V M; Zav'yalov, V P; MacIntyre, S

    1999-04-01

    The periplasmic molecular chaperone Caf1M of Yersinia pestis is a typical representative of a subfamily of specific chaperones involved in assembly of surface adhesins with a very simple structure. One characteristic feature of this Caf1M-like subfamily is possession of an extended, variable sequence (termed FGL) between the F1 and subunit binding G1 beta-strands. In contrast, FGS subfamily members, characterized by PapD, have a short F1-G1 loop and are involved in assembly of complex pili. To elucidate the structural and functional significance of the FGL sequence, a mutant Caf1M molecule (dCaf1M), in which the 27 amino acid residues between the F1 and G1 beta-strands had been deleted, was constructed. Expression of the mutated caf1M in Escherichia coli resulted in accumulation of high levels of dCaf1M. The far-UV circular dichroism spectra of the mutant and wild-type proteins were indistinguishable and exhibited practically the same temperature and pH dependencies. Thus, the FGL sequence of Caf1M clearly does not contribute significantly to the stability of the protein conformation. Preferential cleavage of Caf1M by trypsin at Lys-119 confirmed surface exposure of this part of the FGL sequence in the isolated chaperone and periplasmic chaperone-subunit complex. There was no evidence of surface-localized Caf1 subunit in the presence of the Caf1A outer membrane protein and dCaf1M. In contrast to Caf1M, dCaf1M was not able to form a stable complex with Caf1 nor could it protect the subunit from proteolytic degradation in vivo. This demonstration that the FGL sequence is required for stable chaperone-subunit interaction, but not for folding of a stable chaperone, provides a sound basis for future detailed molecular analyses of the FGL subfamily of chaperones.

  17. Phylogenetic Analysis of the Spider Mite Sub-Family Tetranychinae (Acari: Tetranychidae) Based on the Mitochondrial COI Gene and the 18S and the 5′ End of the 28S rRNA Genes Indicates That Several Genera Are Polyphyletic

    Science.gov (United States)

    Matsuda, Tomoko; Morishita, Maiko; Hinomoto, Norihide; Gotoh, Tetsuo

    2014-01-01

    The spider mite sub-family Tetranychinae includes many agricultural pests. The internal transcribed spacer (ITS) region of nuclear ribosomal RNA genes and the cytochrome c oxidase subunit I (COI) gene of mitochondrial DNA have been used for species identification and phylogenetic reconstruction within the sub-family Tetranychinae, although they have not always been successful. The 18S and 28S rRNA genes should be more suitable for resolving higher levels of phylogeny, such as tribes or genera of Tetranychinae because these genes evolve more slowly and are made up of conserved regions and divergent domains. Therefore, we used both the 18S (1,825–1,901 bp) and 28S (the 5′ end of 646–743 bp) rRNA genes to infer phylogenetic relationships within the sub-family Tetranychinae with a focus on the tribe Tetranychini. Then, we compared the phylogenetic tree of the 18S and 28S genes with that of the mitochondrial COI gene (618 bp). As observed in previous studies, our phylogeny based on the COI gene was not resolved because of the low bootstrap values for most nodes of the tree. On the other hand, our phylogenetic tree of the 18S and 28S genes revealed several well-supported clades within the sub-family Tetranychinae. The 18S and 28S phylogenetic trees suggest that the tribes Bryobiini, Petrobiini and Eurytetranychini are monophyletic and that the tribe Tetranychini is polyphyletic. At the genus level, six genera for which more than two species were sampled appear to be monophyletic, while four genera (Oligonychus, Tetranychus, Schizotetranychus and Eotetranychus) appear to be polyphyletic. The topology presented here does not fully agree with the current morphology-based taxonomy, so that the diagnostic morphological characters of Tetranychinae need to be reconsidered. PMID:25289639

  18. Phylogenetic analysis, structural evolution and functional divergence of the 12-oxo-phytodienoate acid reductase gene family in plants

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    Wang Hongbin

    2009-05-01

    Full Text Available Abstract Background The 12-oxo-phytodienoic acid reductases (OPRs are enzymes that catalyze the reduction of double-bonds in α, β-unsaturated aldehydes or ketones and are part of the octadecanoid pathway that converts linolenic acid to jasmonic acid. In plants, OPRs belong to the old yellow enzyme family and form multigene families. Although discoveries about this family in Arabidopsis and other species have been reported in some studies, the evolution and function of multiple OPRs in plants are not clearly understood. Results A comparative genomic analysis was performed to investigate the phylogenetic relationship, structural evolution and functional divergence among OPR paralogues in plants. In total, 74 OPR genes were identified from 11 species representing the 6 major green plant lineages: green algae, mosses, lycophytes, gymnosperms, monocots and dicots. Phylogenetic analysis showed that seven well-conserved subfamilies exist in plants. All OPR genes from green algae were clustered into a single subfamily, while those from land plants fell into six other subfamilies, suggesting that the events leading to the expansion of the OPR family occurred in land plants. Further analysis revealed that lineage-specific expansion, especially by tandem duplication, contributed to the current OPR subfamilies in land plants after divergence from aquatic plants. Interestingly, exon/intron structure analysis showed that the gene structures of OPR paralogues exhibits diversity in intron number and length, while the intron positions and phase were highly conserved across different lineage species. These observations together with the phylogenetic tree revealed that successive single intron loss, as well as indels within introns, occurred during the process of structural evolution of OPR paralogues. Functional divergence analysis revealed that altered functional constraints have occurred at specific amino acid positions after diversification of the paralogues

  19. 南海分室科单殖吸虫-中国新记录亚科%A NEWLY RECORDED SUBFAMILY OF PSEUDONITZSCHIINAE (MONOGENEA:CAPSALIDAE) IN THE SOUTH CHINA SEA

    Institute of Scientific and Technical Information of China (English)

    杨长平; 邹小梅; 张剑英; 丁雪娟

    2015-01-01

    研究记述寄生于海南清澜绿短臂鱼Aprion virescens鳃上的一种分室科单殖吸虫,短臂鱼蚌盘虫Pseudonitzschia ukuYamaguti,1965。所获标本的形态、量度与Yamaguti(1965)的原始描述基本一致;但南海标本的后吸器上具中央锚钩和边缘小钩等几丁质结构,而 Yamaguti 的描述中无此类结构;原始描述中阴茎表面被向后弯曲的小刺,而南海标本阴茎表面无刺。故此对蚌盘亚科、蚌盘虫属的特征进行了补充修订。该亚科、属及种均为中国新记录。标本保存于华南师范大学生命科学学院鱼类寄生虫学研究室。%A capsalid monogenean,Pseudonitzschia ukuYamaguti,1965, that belongs toPseudonitzschia, Pseudonitzschiinae, was discovered on the gills ofAprion virescens in Qinglan Bay of Hainan in China. The morphology and size of the specimens were consistent with the original description, except that there were anchors and marginal hooklets on their haptor, and that the recurved spines over the cirrus were missing. Therefore here we updated the description of the characteristics of the Pseudonitzschiinae subfamily and thePseudonitzschia genus. The subfamily, genus and species were reported for the first time in China. The specimens were deposited in the Lab of Fish Parasitology of Collage of Life Sciences in the South China Normal University. Amended diagnosis of Pseudonitzschiinae: Capsalidaesensu Yamaguti, 1963. Body elliptical flattened. Haptor disc-shaped, sessile, usually folded antero-posteriorly, armed with one pair of anchors and 14 marginal hooklets; in-dented muscular margin and delicate marginal membrane present; without septa, loculi or papillae. Anterior attachment organ paired, sucker-shaped. One pair of eye spots. Pharynx without constriction. Intestinal limbs with lateral dendritic diverticula, not united posteriorly. Testes numerous, intercecal. Male copulatory pouch muscular, postpharyngeal, con-sisted of ejaculatory and prostatic ducts

  20. Characterization of the starch-acting MaAmyB enzyme from Microbacterium aurum B8.A representing the novel subfamily GH13_42 with an unusual, multi-domain organization

    Science.gov (United States)

    Valk, Vincent; van der Kaaij, Rachel M.; Dijkhuizen, Lubbert

    2016-01-01

    The bacterium Microbacterium aurum strain B8.A degrades granular starches, using the multi-domain MaAmyA α-amylase to initiate granule degradation through pore formation. This paper reports the characterization of the M. aurum B8.A MaAmyB enzyme, a second starch-acting enzyme with multiple FNIII and CBM25 domains. MaAmyB was characterized as an α-glucan 1,4-α-maltohexaosidase with the ability to subsequently hydrolyze maltohexaose to maltose through the release of glucose. MaAmyB also displays exo-activity with a double blocked PNPG7 substrate, releasing PNP. In M. aurum B8.A, MaAmyB may contribute to degradation of starch granules by rapidly hydrolyzing the helical and linear starch chains that become exposed after pore formation by MaAmyA. Bioinformatics analysis showed that MaAmyB represents a novel GH13 subfamily, designated GH13_42, currently with 165 members, all in Gram-positive soil dwelling bacteria, mostly Streptomyces. All members have an unusually large catalytic domain (AB-regions), due to three insertions compared to established α-amylases, and an aberrant C-region, which has only 30% identity to established GH13 C-regions. Most GH13_42 members have three N-terminal domains (2 CBM25 and 1 FNIII). This is unusual as starch binding domains are commonly found at the C-termini of α-amylases. The evolution of the multi-domain M. aurum B8.A MaAmyA and MaAmyB enzymes is discussed. PMID:27808246

  1. Upregulated Expression of Transient Receptor Potential Cation Channel Subfamily V Receptors in Mucosae of Patients with Oral Squamous Cell Carcinoma and Patients with a History of Alcohol Consumption or Smoking

    Science.gov (United States)

    Sakakibara, Akiko; Sakakibara, Shunsuke; Kusumoto, Junya; Takeda, Daisuke; Hasegawa, Takumi; Akashi, Masaya; Minamikawa, Tsutomu; Hashikawa, Kazunobu; Terashi, Hiroto; Komori, Takahide

    2017-01-01

    Objectives Transient receptor potential cation channel (subfamily V, members 1–4) (TRPV1–4) are expressed in skin and neurons and activated by external stimuli in normal mucosae of all oral cavity sites. The oral cavity is exposed to various stimuli, including temperature, mechanical stimuli, chemical substances, and changes in pH, and, notably, the risk factors for oncogenic transformation in oral squamous epithelium are the same as the external stimuli received by TRPV1–4 receptors. Hence, we examined the relationship between oral squamous cell carcinoma (SCC) and TRPV1–4 expression. Materials and Methods Oral SCC patients (n = 37) who underwent surgical resection were included in this study. We investigated the expression of TRPV1–4 by immunohistochemical staining and quantification of TRPV1–4 mRNA in human oral mucosa. In addition, we compared the TRPV1–4 levels in mucosa from patients with SCC to those in normal oral mucosa. Results The receptors were expressed in oral mucosa at all sites (tongue, buccal mucosa, gingiva, and oral floor) and the expression was stronger in epithelia from patients with SCC than in normal epithelia. Furthermore, alcohol consumption and tobacco use were strongly associated with the occurrence of oral cancer and were found to have a remarkable influence on TRPV1–4 receptor expression in normal oral mucosa. In particular, patients with a history of alcohol consumption demonstrated significantly higher expression levels. Conclusion Various external stimuli may influence the behavior of cancer cells. Overexpression of TRPV1-4 is likely to be a factor in enhanced sensitivity to external stimuli. These findings could contribute to the establishment of novel strategies for cancer therapy or prevention. PMID:28081185

  2. Expansion and Functional Divergence of Jumonji C-Containing Histone Demethylases: Significance of Duplications in Ancestral Angiosperms and Vertebrates1[OPEN

    Science.gov (United States)

    Qian, Shengzhan; Wang, Yingxiang

    2015-01-01

    Histone modifications, such as methylation and demethylation, are crucial mechanisms altering chromatin structure and gene expression. Recent biochemical and molecular studies have uncovered a group of histone demethylases called Jumonji C (JmjC) domain proteins. However, their evolutionary history and patterns have not been examined systematically. Here, we report extensive analyses of eukaryotic JmjC genes and define 14 subfamilies, including the Lysine-Specific Demethylase3 (KDM3), KDM5, JMJD6, Putative-Lysine-Specific Demethylase11 (PKDM11), and PKDM13 subfamilies, shared by plants, animals, and fungi. Other subfamilies are detected in plants and animals but not in fungi (PKDM12) or in animals and fungi but not in plants (KDM2 and KDM4). PKDM7, PKDM8, and PKDM9 are plant-specific groups, whereas Jumonji, AT-Rich Interactive Domain2, KDM6, and PKDM10 are animal specific. In addition to known domains, most subfamilies have characteristic conserved amino acid motifs. Whole-genome duplication (WGD) was likely an important mechanism for JmjC duplications, with four pairs from an angiosperm-wide WGD and others from subsequent WGDs. Vertebrates also experienced JmjC duplications associated with the vertebrate ancestral WGDs, with additional mammalian paralogs from tandem duplication and possible transposition. The sequences of paralogs have diverged in both known functional domains and other regions, showing evidence of selection pressure. The increases of JmjC copy number and the divergences in sequence and expression might have contributed to the divergent functions of JmjC genes, allowing the angiosperms and vertebrates to adapt to a great number of ecological niches and contributing to their evolutionary successes. PMID:26059336

  3. Mechanism and Function of Type IV Secretion During Infection of the Human Host.

    Science.gov (United States)

    Gonzalez-Rivera, Christian; Bhatty, Minny; Christie, Peter J

    2016-06-01

    Bacterial pathogens employ type IV secretion systems (T4SSs) for various purposes to aid in survival and proliferation in eukaryotic hosts. One large T4SS subfamily, the conjugation systems, confers a selective advantage to the invading pathogen in clinical settings through dissemination of antibiotic resistance genes and virulence traits. Besides their intrinsic importance as principle contributors to the emergence of multiply drug-resistant "superbugs," detailed studies of these highly tractable systems have generated important new insights into the mode of action and architectures of paradigmatic T4SSs as a foundation for future efforts aimed at suppressing T4SS machine function. Over the past decade, extensive work on the second large T4SS subfamily, the effector translocators, has identified a myriad of mechanisms employed by pathogens to subvert, subdue, or bypass cellular processes and signaling pathways of the host cell. An overarching theme in the evolution of many effectors is that of molecular mimicry. These effectors carry domains similar to those of eukaryotic proteins and exert their effects through stealthy interdigitation of cellular pathways, often with the outcome not of inducing irreversible cell damage but rather of reversibly modulating cellular functions. This article summarizes the major developments for the actively studied pathogens with an emphasis on the structural and functional diversity of the T4SSs and the emerging common themes surrounding effector function in the human host.

  4. Relationship between serum cardiac troponin T level and cardiopulmonary function in stable chronic obstructive pulmonary disease

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    Hattori K

    2015-02-01

    Full Text Available Kumiko Hattori, Takeo Ishii, Takashi Motegi, Yuji Kusunoki, Akihiko Gemma, Kozui Kida Department of Pulmonary Medicine and Oncology; Respiratory Care Clinic, Nippon Medical School, Tokyo, Japan Background: High-sensitivity cardiac troponin T (hs-cTnT in serum is a useful marker of acute myocardial injury, yet information is limited in patients with chronic obstructive pulmonary disease. We aimed to explore the association between hs-cTnT levels and cardiac and pulmonary dysfunction in patients with stable chronic obstructive pulmonary disease and at-risk individuals. Methods: We examined community-dwelling adults with/without chronic obstructive pulmonary disease, with a life-long smoking history, current symptoms of dyspnea during exertion, prolonged coughing, and/or sputum. Serum hs-cTnT concentrations were measured, and subjects underwent pulmonary function tests, high-resolution computed tomography of the chest, an echocardiogram, and a 6-minute walking test. Results: Eighty-six stable patients were identified (mean age 65.5 years; predicted forced expiratory volume in 1 second [FEV1% predicted] 75.0%. Their overall mean hs-cTnT level was 0.008 ng/mL. Logarithmically transformed hs-cTnT levels significantly and positively correlated with age, smoking index, serum high-sensitivity C-reactive protein levels, right ventricle systolic pressure, low attenuation area percentage, and brain natriuretic peptide levels (range r=0.231–0.534, P=0.000 to P=0.042. Further, logarithmically transformed hs-cTnT values significantly and negatively correlated with forced vital capacity, FEV1% predicted, diffusion capacity, arterial oxygen tension, and 6-minute walking distance (range r= -0.482 to -0.377, P=0.000 to P=0.002. Multivariate analyses showed that hs-cTnT values varied independently according to the following three parameters: high-sensitivity C-reactive protein levels (B=0.157, ß=0.450, t=3.571, P=0.001, age (B=0.008, ß=0.352, t=2.789, P=0

  5. Functional multimerization of mucolipin channel proteins.

    Science.gov (United States)

    Curcio-Morelli, Cyntia; Zhang, Peng; Venugopal, Bhuvarahamurthy; Charles, Florie A; Browning, Marsha F; Cantiello, Horacio F; Slaugenhaupt, Susan A

    2010-02-01

    MCOLN1 encodes mucolipin-1 (TRPML1), a member of the transient receptor potential TRPML subfamily of channel proteins. Mutations in MCOLN1 cause mucolipidosis-type IV (MLIV), a lysosomal storage disorder characterized by severe neurologic, ophthalmologic, and gastrointestinal abnormalities. Along with TRPML1, there are two other TRPML family members, mucolipin-2 (TRPML2) and mucolipin-3 (TRPML3). In this study, we used immunocytochemical analysis to determine that TRPML1, TRPML2, and TRPML3 co-localize in cells. The multimerization of TRPML proteins was confirmed by co-immunoprecipitation and Western blot analysis, which demonstrated that TRPML1 homo-multimerizes as well as hetero-multimerizes with TRPML2 and TRPML3. MLIV-causing mutants of TRPML1 also interacted with wild-type TRPML1. Lipid bilayer re-constitution of in vitro translated TRPML2 and TRPML3 confirmed their cation channel properties with lower single channel conductance and higher partial permeability to anions as compared to TRPML1. We further analyzed the electrophysiological properties of single channel TRPML hetero-multimers, which displayed functional differences when compared to individual TRPMLs. Our data shows for the first time that TRPMLs form distinct functional channel complexes. Homo- and hetero-multimerization of TRPMLs may modulate channel function and biophysical properties, thereby increasing TRPML functional diversity.

  6. Functional analysis of the ATP-binding cassette (ABC transporter gene family of Tribolium castaneum

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    Broehan Gunnar

    2013-01-01

    Full Text Available Abstract Background The ATP-binding cassette (ABC transporters belong to a large superfamily of proteins that have important physiological functions in all living organisms. Most are integral membrane proteins that transport a broad spectrum of substrates across lipid membranes. In insects, ABC transporters are of special interest because of their role in insecticide resistance. Results We have identified 73 ABC transporter genes in the genome of T. castaneum, which group into eight subfamilies (ABCA-H. This coleopteran ABC family is significantly larger than those reported for insects in other taxonomic groups. Phylogenetic analysis revealed that this increase is due to gene expansion within a single clade of subfamily ABCC. We performed an RNA interference (RNAi screen to study the function of ABC transporters during development. In ten cases, injection of double-stranded RNA (dsRNA into larvae caused developmental phenotypes, which included growth arrest and localized melanization, eye pigmentation defects, abnormal cuticle formation, egg-laying and egg-hatching defects, and mortality due to abortive molting and desiccation. Some of the ABC transporters we studied in closer detail to examine their role in lipid, ecdysteroid and eye pigment transport. Conclusions The results from our study provide new insights into the physiological function of ABC transporters in T. castaneum, and may help to establish new target sites for insect control.

  7. Functional diversity of human protein kinase splice variants marks significant expansion of human kinome

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    Anamika Krishanpal

    2009-12-01

    Full Text Available Abstract Background Protein kinases are involved in diverse spectrum of cellular processes. Availability of draft version of the human genomic data in the year 2001 enabled recognition of repertoire of protein kinases. However, over the years the human genomic data is being refined and the current release of human genomic data has helped us to recognize a larger repertoire of over 900 human protein kinases represented mainly by splice variants. Results Many of these identified protein kinases are alternatively spliced products. Interestingly, some of the human kinase splice variants appear to be significantly diverged in terms of their functional properties as represented by incorporation or absence of one or more domains. Many sets of protein kinase splice variants have substantially different domain organization and in a few sets of splice variants kinase domains belong to different subfamilies of kinases suggesting potential participation in different signal transduction pathways. Conclusions Addition or deletion of a domain between splice variants of multi-domain kinases appears to be a means of generating differences in the functional features of otherwise similar kinases. It is intriguing that marked sequence diversity within the catalytic regions of some of the splice variant kinases result in kinases belonging to different subfamilies. These human kinase splice variants with different functions might contribute to diversity of eukaryotic cellular signaling.

  8. Two new species of the subfamily Tachininae (Diptera:Tachinidae) from the Liupan Mountains in Ningxia, China%中国宁夏六盘山寄蝇亚科二新种(双翅目:寄蝇科)

    Institute of Scientific and Technical Information of China (English)

    王强; 张春田

    2012-01-01

    记述采自宁夏六盘山区的寄蝇亚科2新种,宁夏透翅寄蝇Hyalurgus ningxiaensis sp.nov.和周氏密克寄蝇Mikia choui sp.nov.,分别隶属埃内寄蝇族Ernestini和寄蝇族Tachinini.宁夏透翅寄蝇外形与分布中国、俄罗斯和欧洲的亮透翅寄蝇H.lucidus相似,但新种额较窄,触角和足股节均黑色,翅r4+5室不闭合,无短柄,明显不同于后者;此外,新种也近似于分布我国的黄足透翅寄蝇H.flavipes,但新种额和颊均较窄,触角基节和梗节黑色,足股节也黑色,腹部第3、4背板均具多对侧心鬃,可区别于后者.周氏密克寄蝇外形与分布我国、印尼及印度的毛缘密克寄蝇M.apicali相似,但新种雌、雄胸部背板中鬃均2+3,翅前缘端半部无黑色斑.R4+5脉从基部到r-m脉段全部具小鬃,后足端位背鬃3根,腹部第1+2合背板无中缘鬃,可区别于后者.新种模式标本保存在沈阳师范大学昆虫标本室.%Two new species of the subfamily Tachininae from the Liupan Mountains in Ningxia,China are found and described:Hyalurgus ningxiaensis sp.nov.and Mikia choui sp.nov..The type specimens are preserved in the Liaoning Key Laboratory of Evolution and Biodiversity of Shenyang Normal University.

  9. Taxonomia da subfamília Corinninae (Araneae, Corinnidae nas regiões neotropical e neártica Taxonomy of the subfamily Corinninae (Araneae, Corinnidae in neotropical and neartic regions

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    Alexandre Bragio Bonaldo

    2000-11-01

    Full Text Available The subfamily Corinninae is characterized and diagnosed. Two synapomorphies are hypothesized for the subfamily, both regarding the male palpal reservoir, which is primarily coiled and presents a sclerotized distal sector. Seventeen genera are recognized, six of which are new: Abapeba (type species Corinna lacertosa Simon, Erendira (type species Corinna pallidoguttata Simon, Septentrinna (type species Corinna bicalcarata Simon, Simonestus (type species Diestus validus Simon, Tapixaua (type species T. callida sp. nov. and Tupirinna (type species T. rosae sp. nov.. The genera Creugas Thorell, Falconina Brignoli and Paradiestus Mello-Leitão are revalidated. Diestus Simon and Lausus Simon are newly synonymized with Corinna C. L. Koch. Chemmis Simon is included in the synonymy of Megalostrata Karsch. Hypsinotus L. Koch is removed from the synonymy of Corinna and included in the synonymy of Creugas. Thirteen new species are described: Septentrinna yucatan and S. potosi from Mexico; Tupirinna rosae from Venezuela and Brazil; Tapixaua callida from Brazil and Peru; Abapeba hoeferi, A. rioclaro, A. taruma, Corinna ducke, C. colombo, C. mourai, C. recurva and Parachemmis manauara from Brazil; Creugas lisei from Brazil, Argentina and Uruguay. Twenty seven species are redescribed. Fifty eight new combinations are presented: from Chemmis, Septentrinna steckleri (Gertsch; from Corinna, Abapeba abalosi (Mello-Leitão, A. cleonei (Petrunkevitch, A. echinus (Simon, A. grassima (Chickering, A. guanicae (Petrunkevitch, A. lacertosa (Simon, A. luctuosa (F. O. Pickard-Cambridge, A. lugubris (Schenkel, A. pennata (Caporiacco, A. kochi (Petrunkevitch, A. saga (F. O. Pickard-Cambridge, A. wheeleri (Petrunkevitch, Creugas annamae (Gertsch & Davis, C. apophysarius (Caporiacco, C. bajulus (Gertsch, C. bellator (L. Koch, C. bicuspis (F.O. Pickard-Cambridge, C. epicureanus (Chamberlin, C. falculus (F. O. Pickard-Cambridge, C. mucronatus (F. O. Pickard-Cambridge, C. navus (F

  10. [Nucleotide receptors--structure and function, history and perspectives].

    Science.gov (United States)

    Barańska, Jolanta

    2014-01-01

    First nucleotide receptors were discovered by Geoffrey Burnstock in 70ties of the last century, as a purinoreceptors activated by ATP. It was further found that they may be activated both by purine and pyrimidine nucleotides and their name was changed to nucleotide receptors. They are divided into two fsamilies: P1, activated by adenosine and P2, activated by nucleotides which are further divided into P2X and P2Y subfamilies. P2X are ionotropic receptors activated by ATP, P2Y (as the P1) are metabotropic receptors coupled with protein G. P2Y receptors are activated by ATP, ADP, UTP, UDP and UDP-sugar derivatives. This review describes early history of extracellular nucleotide signaling studies and presents current knowledge of the particular nucleotide receptors subtypes. The article also describes the structure and functional roles of these receptors and speculates about future research and therapeutic directions in this field.

  11. Duplication and divergence of fgf8 functions in teleost development and evolution.

    Science.gov (United States)

    Jovelin, Richard; He, Xinjun; Amores, Angel; Yan, Yi-Lin; Shi, Ruihua; Qin, Baifang; Roe, Bruce; Cresko, William A; Postlethwait, John H

    2007-12-15

    Fibroblast growth factors play critical roles in many aspects of embryo patterning that are conserved across broad phylogenetic distances. To help understand the evolution of fibroblast growth factor functions, we identified members of the Fgf8/17/18-subfamily in the three-spine stickleback Gasterosteus aculeatus, and investigated their evolutionary relationships and expression patterns. We found that fgf17b is the ortholog of tetrapod Fgf17, whereas the teleost genes called fgf8 and fgf17a are duplicates of the tetrapod gene Fgf8, and thus should be called fgf8a and fgf8b. Phylogenetic analysis supports the view that the Fgf8/17/18-subfamily expanded during the ray-fin fish genome duplication. In situ hybridization experiments showed that stickleback fgf8 duplicates exhibited common and unique expression patterns, indicating that tissue specialization followed the gene duplication event. Moreover, direct comparison of stickleback and zebrafish embryonic expression patterns of fgf8 co-orthologs suggested lineage-specific independent subfunction partitioning and the acquisition or the loss of ortholog functions. In tetrapods, Fgf8 plays an important role in the apical ectodermal ridge of the developing pectoral appendage. Surprisingly, differences in the expression of fgf8a in the apical ectodermal ridge of the pectoral fin bud in zebrafish and stickleback, coupled with the role of fgf16 and fgf24 in teleost pectoral appendage show that different Fgf genes may play similar roles in limb development in various vertebrates.

  12. Accelerated evolution and functional divergence of scorpion short-chain K+ channel toxins after speciation.

    Science.gov (United States)

    Gao, Bin; Zhu, Shunyi

    2012-10-01

    The α-KTx14 subfamily of scorpion toxins is a group of short-chain polypeptides affecting K(+) channels, including five known members which are restrictedly distributed in Mesobuthus martensii. Here, we describe seven new α-KTx14 peptides from M. martensii and its sibling species Mesobuthus eupeus, two of which (termed MarKTX-3 and MeuKTX-1) were chemically synthesized and refolded for structural and functional studies. Electrophysiological recordings of effects of these two peptides on an array of voltage-gated potassium channels revealed that MarKTX-3 was capable of inhibiting five mammalian K(v)1 isoforms (rK(v)1.1-rK(v)1.5) and the Drosophila Shaker channel with low potency whereas MeuKTX-1 lacks such activity. Circular dichroism spectroscopy analysis combined with homology modeling demonstrates that MarKTX-3 and MeuKTX-1 both adopt a similar cysteine-stabilized α-helical and β-sheet fold. Evolutionary analysis indicates accelerated amino acid substitutions in the mature-peptide-encoding regions of orthologous α-KTx14 peptides after speciation, thereby providing evidences for adaptive evolution and functional divergence of this subfamily.

  13. Functional expression of TRPM8 and TRPA1 channels in rat odontoblasts.

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    Maki Tsumura

    Full Text Available Odontoblasts produce dentin during development, throughout life, and in response to pathological conditions by sensing stimulation of exposed dentin. The functional properties and localization patterns of transient receptor potential (TRP melastatin subfamily member 8 (TRPM8 and ankyrin subfamily member 1 (TRPA1 channels in odontoblasts remain to be clarified. We investigated the localization and the pharmacological, biophysical, and mechano-sensitive properties of TRPM8 and TRPA1 channels in rat odontoblasts. Menthol and icilin increased the intracellular free Ca(2+ concentration ([Ca(2+]i. Icilin-, WS3-, or WS12-induced [Ca(2+]i increases were inhibited by capsazepine or 5-benzyloxytriptamine. The increase in [Ca(2+]i elicited by allyl isothiocyanate (AITC was inhibited by HC030031. WS12 and AITC exerted a desensitizing effect on [Ca(2+]i increase. Low-temperature stimuli elicited [Ca(2+]i increases that are sensitive to both 5-benzyloxytriptamine and HC030031. Hypotonic stimulation-induced membrane stretch increased [Ca(2+]i; HC030031 but not 5-benzyloxytriptamine inhibited the effect. The results suggest that TRPM8 channels in rat odontoblasts play a role in detecting low-temperature stimulation of the dentin surface and that TRPA1 channels are involved in sensing membrane stretching and low-temperature stimulation. The results also indicate that odontoblasts act as mechanical and thermal receptor cells, detecting the stimulation of exposed dentin to drive multiple cellular functions, such as sensory transduction.

  14. AtSYP51/52 functions diverge in the post-Golgi traffic and differently affect vacuolar sorting.

    Science.gov (United States)

    De Benedictis, Maria; Bleve, Gianluca; Faraco, Marianna; Stigliano, Egidio; Grieco, Francesco; Piro, Gabriella; Dalessandro, Giuseppe; Di Sansebastiano, Gian Pietro

    2013-05-01

    Plant sensitive factor attachment protein receptors (SNAREs) encoded by genes of the same sub-family are generally considered as redundant in promoting vesicle-associated membrane fusion events. Nonetheless, the application of innovative experimental approaches highlighted that members of the same gene sub-family often have different functional specificities. In this work, two closely related Qc-SNAREs--the AtSYP51 and the AtSYP52--are compared in their ability to influence different secretory pathways. Their role in the vesicle sorting to the central vacuole has been revised and they were found to have a novel inhibitory function. When transiently overexpressed, the SYP51 and the SYP52 distributed between the TGN and the tonoplast. Our data demonstrate that these SYPs (syntaxin of plants) act as t-SNARE when present on the membrane of TGN/PVC, whereas they behave as inhibitory or interfering SNAREs (i-SNAREs) when they accumulate on the tonoplast. Moreover, the performed functional analysis indicated that the AtSYP51 and the AtSYP52 roles differ in the traffic to the vacuole. The findings are a novel contribution to the functional characterization of plant SNAREs that reveals additional non-fusogenic roles.

  15. Molecular clock hypothesis testing based on mitochondrial cytochrome b gene sequence of subfamily bovinae%以牛亚科家畜线粒体细胞色素b基因全序列检验分子钟假说

    Institute of Scientific and Technical Information of China (English)

    耿荣庆; 王兰萍; 常洪; 冀德君; 李永红; 常春芳

    2011-01-01

    To provide some objective data for accepting or refusing molecular clock hypothesis, non-parameter test method was employed based on mitochondrial cytochrome b gene sequence of six species of subfamily bovinae. The complete cytochrome b gene was 1 140 bp in length for all six bovine species and there was a little difference in base composition between species. Transition was the dominant base substitution model and the ratio of transition to transversion was 5.4. The testing results of relative evolution rate based on nucleotide sequences and amino acid sequences showed that molecular clock hypothesis was accepted absolutely within bovine species. The evolution of only a few sequences refused molecular clock hypothesis and evolution of most sequencesaccepted it among the species. It was easier to refuse molecular clock hypothesis based on the testing result from nucleotide sequence than the result from amino acid sequence. There was no obvious correlation between accepting or refusing molecular clock hypothesis and genetic distance between tested species. Molecular clock existed in some species. There was no nucleotide sequence or amino acid sequence varying in an absolutely stable rate in long evolution, and molecular clock was not unicersal.%在测定牛亚科家畜6个物种线粒体细胞色素b(Cyt b)基因全序列的基础上,以非参数检验法检验分子钟假说,提出肯定或否定分子钟假说的部分客观资料.结果表明,6个牛种的Cyt b基因全序列长度都是1140bp,牛种间序列的碱基组成差异较小,碱基替代以转换为主,转换/颠换比为5.4.基于核苷酸序列和氨基酸相对速率检验结果表明,牛种内序列的进化全部接受分子钟假说;牛种问大多数序列的进化接受分子钟假说,少数序列的进化拒绝分子钟假说.与基于氨基酸序列的检验结果相比较,基于核苷酸序列的检验结果更易于拒绝分子钟假说.进而推论,接受或者拒绝分子钟假说与所

  16. Structural and functional diversity of acidic scorpion potassium channel toxins.

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    Zong-Yun Chen

    Full Text Available BACKGROUND: Although the basic scorpion K(+ channel toxins (KTxs are well-known pharmacological tools and potential drug candidates, characterization the acidic KTxs still has the great significance for their potential selectivity towards different K(+ channel subtypes. Unfortunately, research on the acidic KTxs has been ignored for several years and progressed slowly. PRINCIPAL FINDINGS: Here, we describe the identification of nine new acidic KTxs by cDNA cloning and bioinformatic analyses. Seven of these toxins belong to three new α-KTx subfamilies (α-KTx28, α-KTx29, and α-KTx30, and two are new members of the known κ-KTx2 subfamily. ImKTx104 containing three disulfide bridges, the first member of the α-KTx28 subfamily, has a low sequence homology with other known KTxs, and its NMR structure suggests ImKTx104 adopts a modified cystine-stabilized α-helix-loop-β-sheet (CS-α/β fold motif that has no apparent α-helixs and β-sheets, but still stabilized by three disulfide bridges. These newly described acidic KTxs exhibit differential pharmacological effects on potassium channels. Acidic scorpion toxin ImKTx104 was the first peptide inhibitor found to affect KCNQ1 channel, which is insensitive to the basic KTxs and is strongly associated with human cardiac abnormalities. ImKTx104 selectively inhibited KCNQ1 channel with a K(d of 11.69 µM, but was less effective against the basic KTxs-sensitive potassium channels. In addition to the ImKTx104 toxin, HeTx204 peptide, containing a cystine-stabilized α-helix-loop-helix (CS-α/α fold scaffold motif, blocked both Kv1.3 and KCNQ1 channels. StKTx23 toxin, with a cystine-stabilized α-helix-loop-β-sheet (CS-α/β fold motif, could inhibit Kv1.3 channel, but not the KCNQ1 channel. CONCLUSIONS/SIGNIFICANCE: These findings characterize the structural and functional diversity of acidic KTxs, and could accelerate the development and clinical use of acidic KTxs as pharmacological tools and

  17. Evolutionary, structural and functional interplay of the IκB family members.

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    Shaherin Basith

    Full Text Available A primary level of control for nuclear factor kappa B (NF-κB is effected through its interactions with the inhibitor protein, inhibitor of kappa B (IκB. Several lines of evidence confirm the existence of multiple forms of IκB that appear to regulate NF-κB by distinct mechanisms. Therefore, we performed a comprehensive bioinformatics analysis to understand the evolutionary history and intrinsic functional diversity of IκB family members. Phylogenetic relationships were constructed to trace the evolution of the IκB family genes. Our phylogenetic analysis revealed 10 IκB subfamily members that clustered into 5 major clades. Since the ankyrin (ANK domain appears to be more ancient than the Rel homology domain (RHD, our phylogenetic analysis suggests that some undefined ancestral set of ANK repeats acquired an RHD before any duplication and was later duplicated and then diverged into the different IκB subfamilies. Functional analysis identified several functionally divergent sites in the ANK repeat domains (ARDs and revealed that this region has undergone strong purifying selection, suggesting its functional importance in IκB genes. Structural analysis showed that the major variations in the number of ANK repeats and high conformational changes in the finger loop ARD region contribute to the differing binding partner specificities, thereby leading to distinct IκB functions. In summary, our study has provided useful information about the phylogeny and structural and functional divergence of the IκB family. Additionally, we identified a number of amino acid sites that contribute to the predicted functional divergence of these proteins.

  18. Expression and function of P2 receptors in hematopoietic stem and progenitor cells.

    Science.gov (United States)

    Feng, Wenli; Wang, Lina; Zheng, Guoguang

    2015-01-01

    Nucleotides have unambiguously emerged as a family of mediators of intercellular communication, which bind to a class of plasma membrane receptors, P2 receptors, to trigger intercellular signaling. P2 receptors can be further divided into P2X and P2Y subfamilies based on structure and function. Different hematopoietic cells express diverse spectrums of P2 receptors at different levels, including hematopoietic stem and progenitor cells (HSPCs). Extracellular adenosine triphosphate (ATP) exerts different effects on HSPCs, regulating cell proliferation, differentiation, migration, and chemotaxis, release of cytokines or lysosomal constituents, and generation of reactive oxygen or nitrogen species. The relationship between abnormal P2 receptor function and human diseases attracts more and more attention. This review summarizes the expression and function of P2 receptors in HSPCs and the relationship to hematopoietic diseases.

  19. The Drosophila melanogaster methuselah gene: a novel gene with ancient functions.

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    Ana Rita Araújo

    Full Text Available The Drosophila melanogaster G protein-coupled receptor gene, methuselah (mth, has been described as a novel gene that is less than 10 million years old. Nevertheless, it shows a highly specific expression pattern in embryos, larvae, and adults, and has been implicated in larval development, stress resistance, and in the setting of adult lifespan, among others. Although mth belongs to a gene subfamily with 16 members in D. melanogaster, there is no evidence for functional redundancy in this subfamily. Therefore, it is surprising that a novel gene influences so many traits. Here, we explore the alternative hypothesis that mth is an old gene. Under this hypothesis, in species distantly related to D. melanogaster, there should be a gene with features similar to those of mth. By performing detailed phylogenetic, synteny, protein structure, and gene expression analyses we show that the D. virilis GJ12490 gene is the orthologous of mth in species distantly related to D. melanogaster. We also show that, in D. americana (a species of the virilis group of Drosophila, a common amino acid polymorphism at the GJ12490 orthologous gene is significantly associated with developmental time, size, and lifespan differences. Our results imply that GJ12490 orthologous genes are candidates for developmental time and lifespan differences in Drosophila in general.

  20. Functional and Structural Overview of G-Protein-Coupled Receptors Comprehensively Obtained from Genome Sequences

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    Makiko Suwa

    2011-04-01

    Full Text Available An understanding of the functional mechanisms of G-protein-coupled receptors (GPCRs is very important for GPCR-related drug design. We have developed an integrated GPCR database (SEVENS http://sevens.cbrc.jp/ that includes 64,090 reliable GPCR genes comprehensively identified from 56 eukaryote genome sequences, and overviewed the sequences and structure spaces of the GPCRs. In vertebrates, the number of receptors for biological amines, peptides, etc. is conserved in most species, whereas the number of chemosensory receptors for odorant, pheromone, etc. significantly differs among species. The latter receptors tend to be single exon type or a few exon type and show a high ratio in the numbers of GPCRs, whereas some families, such as Class B and Class C receptors, have long lengths due to the presence of many exons. Statistical analyses of amino acid residues reveal that most of the conserved residues in Class A GPCRs are found in the cytoplasmic half regions of transmembrane (TM helices, while residues characteristic to each subfamily found on the extracellular half regions. The 69 of Protein Data Bank (PDB entries of complete or fragmentary structures could be mapped on the TM/loop regions of Class A GPCRs covering 14 subfamilies.

  1. Aquaporin-11: A channel protein lacking apparent transport function expressed in brain

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    Tsunenari Takashi

    2006-05-01

    Full Text Available Abstract Background The aquaporins are a family of integral membrane proteins composed of two subfamilies: the orthodox aquaporins, which transport only water, and the aquaglyceroporins, which transport glycerol, urea, or other small solutes. Two recently described aquaporins, numbers 11 and 12, appear to be more distantly related to the other mammalian aquaporins and aquaglyceroporins. Results We report on the characterization of Aquaporin-11 (AQP11. AQP11 RNA and protein is found in multiple rat tissues, including kidney, liver, testes and brain. AQP11 has a unique distribution in brain, appearing in Purkinje cell dendrites, hippocampal neurons of CA1 and CA2, and cerebral cortical neurons. Immunofluorescent staining of Purkinje cells indicates that AQP11 is intracellular. Unlike other aquaporins, Xenopus oocytes expressing AQP11 in the plasma membrane failed to transport water, glycerol, urea, or ions. Conclusion AQP11 is functionally distinct from other proteins of the aquaporin superfamily and could represent a new aquaporin subfamily. Further studies are necessary to elucidate the role of AQP11 in the brain.

  2. Structural Conservation and Functional Diversity of the Poxvirus Immune Evasion (PIE) Domain Superfamily.

    Science.gov (United States)

    Nelson, Christopher A; Epperson, Megan L; Singh, Sukrit; Elliott, Jabari I; Fremont, Daved H

    2015-08-28

    Poxviruses encode a broad array of proteins that serve to undermine host immune defenses. Structural analysis of four of these seemingly unrelated proteins revealed the recurrent use of a conserved beta-sandwich fold that has not been observed in any eukaryotic or prokaryotic protein. Herein we propose to call this unique structural scaffolding the PIE (Poxvirus Immune Evasion) domain. PIE domain containing proteins are abundant in chordopoxvirinae, with our analysis identifying 20 likely PIE subfamilies among 33 representative genomes spanning 7 genera. For example, cowpox strain Brighton Red appears to encode 10 different PIEs: vCCI, A41, C8, M2, T4 (CPVX203), and the SECRET proteins CrmB, CrmD, SCP-1, SCP-2, and SCP-3. Characterized PIE proteins all appear to be nonessential for virus replication, and all contain signal peptides for targeting to the secretory pathway. The PIE subfamilies differ primarily in the number, size, and location of structural embellishments to the beta-sandwich core that confer unique functional specificities. Reported ligands include chemokines, GM-CSF, IL-2, MHC class I, and glycosaminoglycans. We expect that the list of ligands and receptors engaged by the PIE domain will grow as we come to better understand how this versatile structural architecture can be tailored to manipulate host responses to infection.

  3. Functional conservation between members of an ancient duplicated transcription factor family, LSF/Grainyhead.

    Science.gov (United States)

    Venkatesan, Kavitha; McManus, Heather R; Mello, Craig C; Smith, Temple F; Hansen, Ulla

    2003-08-01

    The LSF/Grainyhead transcription factor family is involved in many important biological processes, including cell cycle, cell growth and development. In order to investigate the evolutionary conservation of these biological roles, we have characterized two new family members in Caenorhabditis elegans and Xenopus laevis. The C.elegans member, Ce-GRH-1, groups with the Grainyhead subfamily, while the X.laevis member, Xl-LSF, groups with the LSF subfamily. Ce-GRH-1 binds DNA in a sequence-specific manner identical to that of Drosophila melanogaster Grainyhead. In addition, Ce-GRH-1 binds to sequences upstream of the C.elegans gene encoding aromatic L-amino-acid decarboxylase and genes involved in post-embryonic development, mab-5 and dbl-1. All three C.elegans genes are homologs of D.melanogaster Grainyhead-regulated genes. RNA-mediated interference of Ce-grh-1 results in embryonic lethality in worms, accompanied by soft, defective cuticles. These phenotypes are strikingly similar to those observed previously in D.melanogaster grainyhead mutants, suggesting conservation of the developmental role of these family members over the course of evolution. Our phylogenetic analysis of the expanded LSF/GRH family (including other previously unrecognized proteins/ESTs) suggests that the structural and functional dichotomy of this family dates back more than 700 million years, i.e. to the time when the first multicellular organisms are thought to have arisen.

  4. Molecular evolution and functional divergence of soluble starch synthase genes in cassava (manihot esculenta crantz).

    Science.gov (United States)

    Yang, Zefeng; Wang, Yifan; Xu, Shuhui; Xu, Chenwu; Yan, Changjie

    2013-01-01

    Soluble starch synthases (SSs) are major enzymes involved in starch biosynthesis in plants. Cassava starch has many remarkable characteristics, which should be influenced by the evolution of SS genes in this starchy root crop. In this work, we performed a comprehensive phylogenetic and evolutionary analysis of the soluble starch synthases in cassava. Genome-wide identification showed that there are 9 genes encoding soluble starch synthases in cassava. All of the soluble starch synthases encoded by these genes contain both Glyco_transf_5 and Glycos_transf_1 domains, and a correlation analysis showed evidence of coevolution between these 2 domains in cassava SS genes. The SS genes in land plants can be divided into 6 subfamilies that were formed before the origin of seed plants, and species-specific expansion has contributed to the evolution of this family in cassava. A functional divergence analysis for this family provided statistical evidence for shifted evolutionary rates between the subfamilies of land plant soluble starch synthases. Although the main selective pressure acting on land plant SS genes was purifying selection, our results also revealed that point mutation with positive selection contributed to the evolution of 2 SS genes in cassava. The remarkable cassava starch characteristics might be the result of both the duplication and adaptive selection of SS genes.

  5. Functional expression of T-type Ca2+ channels in spinal motoneurons of the adult turtle.

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    Martha Canto-Bustos

    Full Text Available Voltage-gated Ca2+ (CaV channels are transmembrane proteins comprising three subfamilies named CaV1, CaV2 and CaV3. The CaV3 channel subfamily groups the low-voltage activated Ca2+ channels (LVA or T-type a significant role in regulating neuronal excitability. CaV3 channel activity may lead to the generation of complex patterns of action potential firing such as the postinhibitory rebound (PIR. In the adult spinal cord, these channels have been found in dorsal horn interneurons where they control physiological events near the resting potential and participate in determining excitability. In motoneurons, CaV3 channels have been found during development, but their functional expression has not yet been reported in adult animals. Here, we show evidence for the presence of CaV3 channel-mediated PIR in motoneurons of the adult turtle spinal cord. Our results indicate that Ni2+ and NNC55-0396, two antagonists of CaV3 channel activity, inhibited PIR in the adult turtle spinal cord. Molecular biology and biochemical assays revealed the expression of the CaV3.1 channel isotype and its localization in motoneurons. Together, these results provide evidence for the expression of CaV3.1 channels in the spinal cord of adult animals and show also that these channels may contribute to determine the excitability of motoneurons.

  6. Identification and functional analysis of olfactory receptor family reveal unusual characteristics of the olfactory system in the migratory locust.

    Science.gov (United States)

    Wang, Zhifeng; Yang, Pengcheng; Chen, Dafeng; Jiang, Feng; Li, Yan; Wang, Xianhui; Kang, Le

    2015-11-01

    Locusts represent the excellent model of insect olfaction because the animals are equipped with an unusual olfactory system and display remarkable density-dependent olfactory plasticity. However, information regarding receptor molecules involved in the olfactory perception of locusts is very limited. On the basis of genome sequence and antennal transcriptome of the migratory locust, we conduct the identification and functional analysis of two olfactory receptor families: odorant receptors (ORs) and ionotropic receptors (IRs). In the migratory locust, there is an expansion of OR family (142 ORs) while distinctly lower number of IR genes (32 IRs) compared to the repertoires of other insects. The number of the locust OR genes is much less than that of glomeruli in antennal lobe, challenging the general principle of the "one glomerulus-one receptor" observed in other insects. Most OR genes are found in tandem arrays, forming two large lineage-specific subfamilies in the phylogenetic tree. The "divergent IR" subfamily displays a significant contraction, and most of the IRs belong to the "antennal IR" subfamily in the locust. Most ORs/IRs have olfactory-specific expression while some broadly- or internal-expressed members are also found. Differing from holometabolous insects, the migratory locust contains very similar expression profiles of ORs/IRs between nymph and adult stages. RNA interference and behavioral assays indicate that an OR-based signaling pathway, not IR-based, mediates the attraction of locusts to aggregation pheromones. These discoveries provide insights into the unusual olfactory system of locusts and enhance our understanding of the evolution of insect olfaction.

  7. GTPase domains of ras p21 oncogene protein and elongation factor Tu: analysis of three-dimensional structures, sequence families, and functional sites.

    Science.gov (United States)

    Valencia, A; Kjeldgaard, M; Pai, E F; Sander, C

    1991-06-15

    GTPase domains are functional and structural units employed as molecular switches in a variety of important cellular functions, such as growth control, protein biosynthesis, and membrane traffic. Amino acid sequences of more than 100 members of different subfamilies are known, but crystal structures of only mammalian ras p21 and bacterial elongation factor Tu have been determined. After optimal superposition of these remarkably similar structures, careful multiple sequence alignment, and calculation of residue-residue interactions, we analyzed the two subfamilies in terms of structural conservation, sequence conservation, and residue contact strength. There are three main results. (i) A structure-based alignment of p21 and elongation factor Tu. (ii) The definition of a common conserved structural core that may be useful as the basis of model building by homology of the three-dimensional structure of any GTPase domain. (iii) Identification of sequence regions, other than the effector loop and the nucleotide binding site, that may be involved in the functional cycle: they are loop L4, known to change conformation after GTP hydrolysis; helix alpha 2, especially Arg-73 and Met-67 in ras p21; loops L8 and L10, including ras p21 Arg-123, Lys-147, and Leu-120; and residues located spatially near the N and C termini. These regions are candidate sites for interaction either with the GTP/GDP exchange factor, with a GTPase-affected function, or with a molecule delivered to a destination site with the aid of the GTPase domain.

  8. Functions and Application of the AP2/ERF Transcription Factor Family in Crop Improvement

    Institute of Scientific and Technical Information of China (English)

    Zhao-Shi Xu; Ming Chen; Lian-Cheng Li; You-Zhi Ma

    2011-01-01

    Plants have acquired sophisticated stress response systems to adapt to changing environments. It is important to understand plants' stress response mechanisms in the effort to improve crop productivity under stressful conditions. The AP2/ERF transcription factors are known to regulate diverse processes of plant development and stress responses.In this study, the molecular characteristics and biological functions of AP2/ERFs in a variety of plant species were analyzed. AP2/ERFs,especially those in DREB and ERF subfamilies, are ideal candidates for crop improvement because their overexpression enhances tolerances to drought, salt, freezing, as well as resistances to multiple diseases in the transgenic plants. The comprehensive analysis of physiological functions is useful in elucidating the biological roles of AP2/ERF family genes in gene interaction, pathway regulation, and defense response under stress environments, which should provide new opportunities for the crop tolerance engineering.

  9. Inferring hypotheses on functional relationships of genes: Analysis of the Arabidopsis thaliana subtilase gene family.

    Directory of Open Access Journals (Sweden)

    Carsten Rautengarten

    2005-09-01

    Full Text Available The gene family of subtilisin-like serine proteases (subtilases in Arabidopsis thaliana comprises 56 members, divided into six distinct subfamilies. Whereas the members of five subfamilies are similar to pyrolysins, two genes share stronger similarity to animal kexins. Mutant screens confirmed 144 T-DNA insertion lines with knockouts for 55 out of the 56 subtilases. Apart from SDD1, none of the confirmed homozygous mutants revealed any obvious visible phenotypic alteration during growth under standard conditions. Apart from this specific case, forward genetics gave us no hints about the function of the individual 54 non-characterized subtilase genes. Therefore, the main objective of our work was to overcome the shortcomings of the forward genetic approach and to infer alternative experimental approaches by using an integrative bioinformatics and biological approach. Computational analyses based on transcriptional co-expression and co-response pattern revealed at least two expression networks, suggesting that functional redundancy may exist among subtilases with limited similarity. Furthermore, two hubs were identified, which may be involved in signalling or may represent higher-order regulatory factors involved in responses to environmental cues. A particular enrichment of co-regulated genes with metabolic functions was observed for four subtilases possibly representing late responsive elements of environmental stress. The kexin homologs show stronger associations with genes of transcriptional regulation context. Based on the analyses presented here and in accordance with previously characterized subtilases, we propose three main functions of subtilases: involvement in (i control of development, (ii protein turnover, and (iii action as downstream components of signalling cascades. Supplemental material is available in the Plant Subtilase Database (PSDB (http://csbdb.mpimp-golm.mpg.de/psdb.html, as well as from the CSB.DB (http://csbdb.mpimp-golm.mpg.de.

  10. Inferring Hypotheses on Functional Relationships of Genes: Analysis of the Arabidopsis thaliana Subtilase Gene Family.

    Directory of Open Access Journals (Sweden)

    2005-09-01

    Full Text Available The gene family of subtilisin-like serine proteases (subtilases in Arabidopsis thaliana comprises 56 members, divided into six distinct subfamilies. Whereas the members of five subfamilies are similar to pyrolysins, two genes share stronger similarity to animal kexins. Mutant screens confirmed 144 T-DNA insertion lines with knockouts for 55 out of the 56 subtilases. Apart from SDD1, none of the confirmed homozygous mutants revealed any obvious visible phenotypic alteration during growth under standard conditions. Apart from this specific case, forward genetics gave us no hints about the function of the individual 54 non-characterized subtilase genes. Therefore, the main objective of our work was to overcome the shortcomings of the forward genetic approach and to infer alternative experimental approaches by using an integrative bioinformatics and biological approach. Computational analyses based on transcriptional co-expression and co-response pattern revealed at least two expression networks, suggesting that functional redundancy may exist among subtilases with limited similarity. Furthermore, two hubs were identified, which may be involved in signalling or may represent higher-order regulatory factors involved in responses to environmental cues. A particular enrichment of co-regulated genes with metabolic functions was observed for four subtilases possibly representing late responsive elements of environmental stress. The kexin homologs show stronger associations with genes of transcriptional regulation context. Based on the analyses presented here and in accordance with previously characterized subtilases, we propose three main functions of subtilases: involvement in (i control of development, (ii protein turnover, and (iii action as downstream components of signalling cascades. Supplemental material is available in the Plant Subtilase Database (PSDB (http://csbdb.mpimp-golm.mpg.de/psdb.html , as well as from the CSB.DB (http://csbdb.mpimp-golm.mpg.de.

  11. Assessing the ability of sequence-based methods to provide functional insight within membrane integral proteins: a case study analyzing the neurotransmitter/Na+ symporter family

    Directory of Open Access Journals (Sweden)

    Eskandari Sepehr

    2007-10-01

    Full Text Available Abstract Background Efforts to predict functional sites from globular proteins is increasingly common; however, the most successful of these methods generally require structural insight. Unfortunately, despite several recent technological advances, structural coverage of membrane integral proteins continues to be sparse. ConSequently, sequence-based methods represent an important alternative to illuminate functional roles. In this report, we critically examine the ability of several computational methods to provide functional insight within two specific areas. First, can phylogenomic methods accurately describe the functional diversity across a membrane integral protein family? And second, can sequence-based strategies accurately predict key functional sites? Due to the presence of a recently solved structure and a vast amount of experimental mutagenesis data, the neurotransmitter/Na+ symporter (NSS family is an ideal model system to assess the quality of our predictions. Results The raw NSS sequence dataset contains 181 sequences, which have been aligned by various methods. The resultant phylogenetic trees always contain six major subfamilies are consistent with the functional diversity across the family. Moreover, in well-represented subfamilies, phylogenetic clustering recapitulates several nuanced functional distinctions. Functional sites are predicted using six different methods (phylogenetic motifs, two methods that identify subfamily-specific positions, and three different conservation scores. A canonical set of 34 functional sites identified by Yamashita et al. within the recently solved LeuTAa structure is used to assess the quality of the predictions, most of which are predicted by the bioinformatic methods. Remarkably, the importance of these sites is largely confirmed by experimental mutagenesis. Furthermore, the collective set of functional site predictions qualitatively clusters along the proposed transport pathway, further

  12. Structure-Function Analysis of a Mixed-linkage β-Glucanase/Xyloglucanase from the Key Ruminal Bacteroidetes Prevotella bryantii B(1)4.

    Science.gov (United States)

    McGregor, Nicholas; Morar, Mariya; Fenger, Thomas Hauch; Stogios, Peter; Lenfant, Nicolas; Yin, Victor; Xu, Xiaohui; Evdokimova, Elena; Cui, Hong; Henrissat, Bernard; Savchenko, Alexei; Brumer, Harry

    2016-01-15

    The recent classification of glycoside hydrolase family 5 (GH5) members into subfamilies enhances the prediction of substrate specificity by phylogenetic analysis. However, the small number of well characterized members is a current limitation to understanding the molecular basis of the diverse specificity observed across individual GH5 subfamilies. GH5 subfamily 4 (GH5_4) is one of the largest, with known activities comprising (carboxymethyl)cellulases, mixed-linkage endo-glucanases, and endo-xyloglucanases. Through detailed structure-function analysis, we have revisited the characterization of a classic GH5_4 carboxymethylcellulase, PbGH5A (also known as Orf4, carboxymethylcellulase, and Cel5A), from the symbiotic rumen Bacteroidetes Prevotella bryantii B14. We demonstrate that carboxymethylcellulose and phosphoric acid-swollen cellulose are in fact relatively poor substrates for PbGH5A, which instead exhibits clear primary specificity for the plant storage and cell wall polysaccharide, mixed-linkage β-glucan. Significant activity toward the plant cell wall polysaccharide xyloglucan was also observed. Determination of PbGH5A crystal structures in the apo-form and in complex with (xylo)glucan oligosaccharides and an active-site affinity label, together with detailed kinetic analysis using a variety of well defined oligosaccharide substrates, revealed the structural determinants of polysaccharide substrate specificity. In particular, this analysis highlighted the PbGH5A active-site motifs that engender predominant mixed-linkage endo-glucanase activity vis à vis predominant endo-xyloglucanases in GH5_4. However the detailed phylogenetic analysis of GH5_4 members did not delineate particular clades of enzymes sharing these sequence motifs; the phylogeny was instead dominated by bacterial taxonomy. Nonetheless, our results provide key enzyme functional and structural reference data for future bioinformatics analyses of (meta)genomes to elucidate the biology of

  13. Functional Boxplots

    KAUST Repository

    Sun, Ying

    2011-01-01

    This article proposes an informative exploratory tool, the functional boxplot, for visualizing functional data, as well as its generalization, the enhanced functional boxplot. Based on the center outward ordering induced by band depth for functional data, the descriptive statistics of a functional boxplot are: the envelope of the 50% central region, the median curve, and the maximum non-outlying envelope. In addition, outliers can be detected in a functional boxplot by the 1.5 times the 50% central region empirical rule, analogous to the rule for classical boxplots. The construction of a functional boxplot is illustrated on a series of sea surface temperatures related to the El Niño phenomenon and its outlier detection performance is explored by simulations. As applications, the functional boxplot and enhanced functional boxplot are demonstrated on children growth data and spatio-temporal U.S. precipitation data for nine climatic regions, respectively. This article has supplementary material online. © 2011 American Statistical Association.

  14. Analysis of TIR- and non-TIR-NBS-LRR disease resistance gene analogous in pepper: characterization, genetic variation, functional divergence and expression patterns

    Directory of Open Access Journals (Sweden)

    Wan Hongjian

    2012-09-01

    Full Text Available Abstract Background Pepper (Capsicum annuum L. is one of the most important vegetable crops worldwide. However, its yield and fruit quality can be severely threatened by several pathogens. The plant nucleotide-binding site (NBS-leucine-rich repeat (LRR gene family is the largest class of known disease resistance genes (R genes effective against such pathogens. Therefore, the isolation and identification of such R gene homologues from pepper will provide a critical foundation for improving disease resistance breeding programs. Results A total of 78 R gene analogues (CaRGAs were identified in pepper by degenerate PCR amplification and database mining. Phylogenetic tree analysis of the deduced amino acid sequences for 51 of these CaRGAs with typically conserved motifs ( P-loop, kinase-2 and GLPL along with some known R genes from Arabidopsis and tomato grouped these CaRGAs into the non-Toll interleukin-1 receptor (TIR-NBS-LRR (CaRGAs I to IV and TIR-NBS-LRR (CaRGAs V to VII subfamilies. The presence of consensus motifs (i.e. P-loop, kinase-2 and hydrophobic domain is typical of the non-TIR- and TIR-NBS-LRR gene subfamilies. This finding further supports the view that both subfamilies are widely distributed in dicot species. Functional divergence analysis provided strong statistical evidence of altered selective constraints during protein evolution between the two subfamilies. Thirteen critical amino acid sites involved in this divergence were also identified using DIVERGE version 2 software. Analyses of non-synonymous and synonymous substitutions per site showed that purifying selection can play a critical role in the evolutionary processes of non-TIR- and TIR-NBS-LRR RGAs in pepper. In addition, four specificity-determining positions were predicted to be responsible for functional specificity. qRT-PCR analysis showed that both salicylic and abscisic acids induce the expression of CaRGA genes, suggesting that they may primarily be involved in

  15. Functionalized Calixpyrroles

    DEFF Research Database (Denmark)

    Vargas-Zúñiga, Gabriela; Sessler, Jonathan; Bähring, Steffen

    2016-01-01

    as the extraction and transport of anionic species and ion pairs including cesium halide and sulfate salts. It is divided into seven sections. The first section describes the synthetic methods employed to functionalized calix[4]pyrrole. The second section focuses on functionalized calix[4]pyrroles that display...... enhanced anion binding properties compared to the non-functionalized parent system, octamethylcalix[4]pyrrole. The use of functionalized calix[4]pyrroles containing a fluorescent group or functionalized calix[4]pyrroles as building blocks for the preparation of stimulus-responsive materials is discussed...... and the eventual development of therapeutics that function via the transport of anions across cell membranes, are discussed....

  16. Functional Characterization of Sesquiterpene Synthase from Polygonum minus

    Directory of Open Access Journals (Sweden)

    Su-Fang Ee

    2014-01-01

    Full Text Available Polygonum minus is an aromatic plant, which contains high abundance of terpenoids, especially the sesquiterpenes C15H24. Sesquiterpenes were believed to contribute to the many useful biological properties in plants. This study aimed to functionally characterize a full length sesquiterpene synthase gene from P. minus. P. minus sesquiterpene synthase (PmSTS has a complete open reading frame (ORF of 1689 base pairs encoding a 562 amino acid protein. Similar to other sesquiterpene synthases, PmSTS has two large domains: the N-terminal domain and the C-terminal metal-binding domain. It also consists of three conserved motifs: the DDXXD, NSE/DTE, and RXR. A three-dimensional protein model for PmSTS built clearly distinguished the two main domains, where conserved motifs were highlighted. We also constructed a phylogenetic tree, which showed that PmSTS belongs to the angiosperm sesquiterpene synthase subfamily Tps-a. To examine the function of PmSTS, we expressed this gene in Arabidopsis thaliana. Two transgenic lines, designated as OE3 and OE7, were further characterized, both molecularly and functionally. The transgenic plants demonstrated smaller basal rosette leaves, shorter and fewer flowering stems, and fewer seeds compared to wild type plants. Gas chromatography-mass spectrometry analysis of the transgenic plants showed that PmSTS was responsible for the production of β-sesquiphellandrene.

  17. Entire functions

    CERN Document Server

    Markushevich, A I

    1966-01-01

    Entire Functions focuses on complex numbers and the algebraic operations on them and the basic principles of mathematical analysis.The book first elaborates on the concept of an entire function, including the natural generalization of the concept of a polynomial and power series. The text then takes a look at the maximum absolute value and the order of an entire function, as well as calculations for the coefficients of power series representing a given function, use of integrals, and complex numbers. The publication elaborates on the zeros of an entire function and the fundamen

  18. Functionalized amphipols

    DEFF Research Database (Denmark)

    Della Pia, Eduardo Antonio; Hansen, Randi Westh; Zoonens, Manuela

    2014-01-01

    Amphipols are amphipathic polymers that stabilize membrane proteins isolated from their native membrane. They have been functionalized with various chemical groups in the past years for protein labeling and protein immobilization. This large toolbox of functionalized amphipols combined with their......Amphipols are amphipathic polymers that stabilize membrane proteins isolated from their native membrane. They have been functionalized with various chemical groups in the past years for protein labeling and protein immobilization. This large toolbox of functionalized amphipols combined...... surfaces for various applications in synthetic biology. This review summarizes the properties of functionalized amphipols suitable for synthetic biology approaches....

  19. Lightness functions

    DEFF Research Database (Denmark)

    Campi, Stefano; Gardner, Richard; Gronchi, Paolo;

    2012-01-01

    Variants of the brightness function of a convex body K in n-dimensional Euclidean are investigated. The Lambertian lightness function L(K; v , w ) gives the total reflected light resulting from illumination by a light source at infinity in the direction w that is visible when looking...... in the direction v . The partial brightness function R( K ; v , w ) gives the area of the projection orthogonal to v of the portion of the surface of K that is both illuminated by a light source from the direction w and visible when looking in the direction v . A class of functions called lightness functions...... is introduced that includes L(K;.) and R(K;.) as special cases. Much of the theory of the brightness function like uniqueness, stability, and the existence and properties of convex bodies of maximal and minimal volume with finitely many function values equal to those of a given convex body, is extended...

  20. Function-Based Metagenomic Library Screening and Heterologous Expression Strategy for Genes Encoding Phosphatase Activity.

    Science.gov (United States)

    Villamizar, Genis A Castillo; Nacke, Heiko; Daniel, Rolf

    2017-01-01

    The release of phosphate from inorganic and organic phosphorus compounds can be mediated enzymatically. Phosphate-releasing enzymes, comprising acid and alkaline phosphatases, are recognized as useful biocatalysts in applications such as plant and animal nutrition, bioremediation and diagnostic analysis. Metagenomic approaches provide access to novel phosphatase-encoding genes. Here, we describe a function-based screening approach for rapid identification of genes conferring phosphatase activity from small-insert and large-insert metagenomic libraries derived from various environments. This approach bears the potential for discovery of entirely novel phosphatase families or subfamilies and members of known enzyme classes hydrolyzing phosphomonoester bonds such as phytases. In addition, we provide a strategy for efficient heterologous phosphatase gene expression.

  1. Two-pore channels (TPCs): Novel voltage-gated ion channels with pleiotropic functions.

    Science.gov (United States)

    Feijóo-Bandín, Sandra; García-Vence, María; García-Rúa, Vanessa; Roselló-Lletí, Esther; Portolés, Manuel; Rivera, Miguel; González-Juanatey, José Ramón; Lago, Francisca

    2017-01-02

    Two-pore channels (TPC1-3) comprise a subfamily of the eukaryotic voltage-gated ion channels (VGICs) superfamily that are mainly expressed in acidic stores in plants and animals. TPCS are widespread across the animal kingdom, with primates, mice and rats lacking TPC3, and mainly act as Ca(+) and Na(+) channels, although it was also suggested that they could be permeable to other ions. Nowadays, TPCs have been related to the development of different diseases, including Parkinson´s disease, obesity or myocardial ischemia. Due to this, their study has raised the interest of the scientific community to try to understand their mechanism of action in order to be able to develop an efficient drug that could regulate TPCs activity. In this review, we will provide an updated view regarding TPCs structure, function and activation, as well as their role in different pathophysiological processes.

  2. Functional morphology and biomechanics of branch-stem junctions in columnar cacti.

    Science.gov (United States)

    Schwager, Hannes; Masselter, Tom; Speck, Thomas; Neinhuis, Christoph

    2013-12-07

    Branching in columnar cacti features morphological and anatomical characteristics specific to the subfamily Cactoideae. The most conspicuous features are the pronounced constrictions at the branch-stem junctions, which are also present in the lignified vascular structures within the succulent cortex. Based on finite-element analyses of ramification models, we demonstrate that these indentations in the region of high flexural and torsional stresses are not regions of structural weakness (e.g. allowing vegetative propagation). On the contrary, they can be regarded as anatomical adaptations to increase the stability by fine-tuning the stress state and stress directions in the junction along prevalent fibre directions. Biomimetic adaptations improving the functionality of ramifications in technical components, inspired, in particular, by the fine-tuned geometrical shape and arrangement of lignified strengthening tissues of biological role models, might contribute to the development of alternative concepts for branched fibre-reinforced composite structures within a limited design space.

  3. Functional morphology and biomechanics of branch–stem junctions in columnar cacti

    Science.gov (United States)

    Schwager, Hannes; Masselter, Tom; Speck, Thomas; Neinhuis, Christoph

    2013-01-01

    Branching in columnar cacti features morphological and anatomical characteristics specific to the subfamily Cactoideae. The most conspicuous features are the pronounced constrictions at the branch–stem junctions, which are also present in the lignified vascular structures within the succulent cortex. Based on finite-element analyses of ramification models, we demonstrate that these indentations in the region of high flexural and torsional stresses are not regions of structural weakness (e.g. allowing vegetative propagation). On the contrary, they can be regarded as anatomical adaptations to increase the stability by fine-tuning the stress state and stress directions in the junction along prevalent fibre directions. Biomimetic adaptations improving the functionality of ramifications in technical components, inspired, in particular, by the fine-tuned geometrical shape and arrangement of lignified strengthening tissues of biological role models, might contribute to the development of alternative concepts for branched fibre-reinforced composite structures within a limited design space. PMID:24132310

  4. The expression and function of organic anion transporting polypeptides in normal tissues and in cancer.

    Science.gov (United States)

    Obaidat, Amanda; Roth, Megan; Hagenbuch, Bruno

    2012-01-01

    Organic anion transporting polypeptides (OATPs) are members of the SLCO gene superfamily of proteins. The 11 human OATPs are classified into 6 families and subfamilies on the basis of their amino acid sequence similarities. OATPs are expressed in several epithelial tissues throughout the body and transport mainly amphipathic molecules with molecular weights of more than 300 kDa. Members of the OATP1 and OATP2 families are functionally the best-characterized OATPs. Among these are the multispecific OATP1A2, OATP1B1, OATP1B3, and OATP2B1. They transport various endo- and xenobiotics, including hormones and their conjugates as well as numerous drugs such as several anticancer agents. Recent reports demonstrate that some OATPs are up- or downregulated in several cancers and that OATP expression might affect cancer development. On the basis of the findings summarized in this review, we propose that OATPs could be valuable targets for anticancer therapy.

  5. A plethora of plant serine/arginine-rich proteins: redundancy or evolution of novel gene functions?

    Science.gov (United States)

    Kalyna, Maria; Barta, Andrea

    2017-01-01

    Pre-mRNA processing is an important step in gene expression and its regulation leads to the expansion of the gene product repertoire. Serine/arginine-rich (SR) proteins are key players in intron recognition and spliceosome assembly and contribute significantly to the alternative splicing process. Due to several duplication events, at least 19 SR proteins are present in the Arabidopsis genome which is almost twice as much as in humans. They fall into seven different subfamilies, three of them homologous to metazoan splicing factors whereas the other four seem to be specific for plants. The current data show that most duplicated genes have different spatio-temporal expression patterns indicating functional diversification. Interestingly, the majority of SR protein genes are alternatively spliced and in some cases this process was shown to be under developmental and/or environmental control. This might greatly influence gene expression of target genes as also exemplified by ectopic expression studies of particular SR proteins. PMID:15270675

  6. Functional analysis

    CERN Document Server

    Kantorovich, L V

    1982-01-01

    Functional Analysis examines trends in functional analysis as a mathematical discipline and the ever-increasing role played by its techniques in applications. The theory of topological vector spaces is emphasized, along with the applications of functional analysis to applied analysis. Some topics of functional analysis connected with applications to mathematical economics and control theory are also discussed. Comprised of 18 chapters, this book begins with an introduction to the elements of the theory of topological spaces, the theory of metric spaces, and the theory of abstract measure space

  7. Molecular Evolution and Functional Divergence of Trace Amine-Associated Receptors.

    Directory of Open Access Journals (Sweden)

    Seong-Il Eyun

    Full Text Available Trace amine-associated receptors (TAARs are a member of the G-protein-coupled receptor superfamily and are known to be expressed in olfactory sensory neurons. A limited number of molecular evolutionary studies have been done for TAARs so far. To elucidate how lineage-specific evolution contributed to their functional divergence, we examined 30 metazoan genomes. In total, 493 TAAR gene candidates (including 84 pseudogenes were identified from 26 vertebrate genomes. TAARs were not identified from non-vertebrate genomes. An ancestral-type TAAR-like gene appeared to have emerged in lamprey. We found four therian-specific TAAR subfamilies (one eutherian-specific and three metatherian-specific in addition to previously known nine subfamilies. Many species-specific TAAR gene duplications and losses contributed to a large variation of TAAR gene numbers among mammals, ranging from 0 in dolphin to 26 in flying fox. TAARs are classified into two groups based on binding preferences for primary or tertiary amines as well as their sequence similarities. Primary amine-detecting TAARs (TAAR1-4 have emerged earlier, generally have single-copy orthologs (very few duplication or loss, and have evolved under strong functional constraints. In contrast, tertiary amine-detecting TAARs (TAAR5-9 have emerged more recently and the majority of them experienced higher rates of gene duplications. Protein members that belong to the tertiary amine-detecting TAAR group also showed the patterns of positive selection especially in the area surrounding the ligand-binding pocket, which could have affected ligand-binding activities and specificities. Expansions of the tertiary amine-detecting TAAR gene family may have played important roles in terrestrial adaptations of therian mammals. Molecular evolution of the TAAR gene family appears to be governed by a complex, species-specific, interplay between environmental and evolutionary factors.

  8. Stability Functions

    CERN Document Server

    Burns, Daniel; Wang, Zuoqin

    2008-01-01

    In this article we discuss the role of stability functions in geometric invariant theory and apply stability function techniques to problems in toric geometry. In particular we show how one can use these techniques to recover results of Burns-Guillemin-Uribe and Shiffman-Tate-Zelditch on asymptotic properties of sections of holomorphic line bundles over toric varieties.

  9. POWER FUNCTIONS

    Institute of Scientific and Technical Information of China (English)

    王雷

    2008-01-01

    <正>A power function of degree n is a function of the form f(x)=ax~n.For large n,it appears that the graph coincide with the x-axis near the origin,but it does not;the graph actually touches the x—axis only at the origin.

  10. Flow cytometric analyses of the viability, surface marker expression and function of lymphocytes from children following cryopreservation.

    Science.gov (United States)

    Chen, Xi; Zhang, Hui; Mou, Wenjun; Qi, Zhan; Ren, Xiaoya; Wang, Guoliang; Jiao, Hong; Kong, Xiaohui; Gui, Jingang

    2016-11-01

    Flow cytometric analysis is important for the investigation and clinical preparation of lymphocytes from children. However, the strict requirement of cell freshness and inter‑assay variability limits the application of this methodology for pediatric investigations. Therefore, it is necessary to identify a reliable cryopreservative method capable of maintaining high cell viability and proper cell function in lymphocytes from children. In the present study, eight commonly‑used cell cyropreservative methods were used, and their effects on cell viability, surface marker expression and cell function were examined. In addition, how these methods affect the distribution of T‑cell receptor Vβ subfamilies were also determined. The results of the present study provided valuable experimental evidence, based on which the optimal method for the cryopreservation of lymphocytes from children in pediatric investigations and clinical applications can be selected.

  11. CARDINAL FUNCTIONS AND INTEGRAL FUNCTIONS

    OpenAIRE

    MIRCEA E. ŞELARIU; FLORENTIN SMARANDACHE; MARIAN NIŢU

    2015-01-01

    This paper presents the correspondences of the eccentric mathematics of cardinal and integral functions and centric mathematics, or ordinary mathematics. Centric functions will also be presented in the introductory section, because they are, although widely used in undulatory physics, little known.

  12. CARDINAL FUNCTIONS AND INTEGRAL FUNCTIONS

    OpenAIRE

    MIRCEA E. ŞELARIU; FLORENTIN SMARANDACHE; MARIAN NIŢU

    2015-01-01

    This paper presents the correspondences of the eccentric mathematics of cardinal and integral functions and centric mathematics, or ordinary mathematics. Centric functions will also be presented in the introductory section, because they are, although widely used in undulatory physics, little known.

  13. Ecosystem functioning

    National Research Council Canada - National Science Library

    Jax, Kurt

    2010-01-01

    "In the face of decreasing biodiversity and ongoing global changes, maintaining ecosystem functioning is seen both as a means to preserve biological diversity as well as for safeguarding human well...

  14. Transfer functions

    Science.gov (United States)

    Taback, I.

    1979-01-01

    The vulnerability of electronic equipment to carbon fibers is studied. The effectiveness of interfaces, such as filters, doors, window screens, and cabinets, which affect the concentration, exposure, or deposition of carbon fibers on both (internal and external) sides of the interface is examined. The transfer function of multilayer aluminum mesh, wet and dry, polyurethane foam, and window screen are determined as a function of air velocity. FIlters installed in typical traffic control boxes and air conditioners are also considered.

  15. Functional Unparsing

    DEFF Research Database (Denmark)

    Danvy, Olivier

    1998-01-01

    A string-formatting function such as printf in C seemingly requires dependent types, because its control string determines the rest of its arguments. We show how changing the representation of the control string makes it possible to program printf in ML (which does not allow dependent types......). The result is well typed and perceptibly more efficient than the corresponding library functions in Standard ML of New Jersey and in Caml....

  16. Functional unparsing

    DEFF Research Database (Denmark)

    Danvy, Olivier

    2000-01-01

    A string-formatting function such as printf in C seemingly requires dependent types, because its control string determines the rest of its arguments. Examples: formula here We show how changing the representation of the control string makes it possible to program printf in ML (which does not allow...... dependent types). The result is well typed and perceptibly more efficient than the corresponding library functions in Standard ML of New Jersey and in Caml....

  17. Multiple Functions of Let-23, a Caenorhabditis Elegans Receptor Tyrosine Kinase Gene Required for Vulval Induction

    Science.gov (United States)

    Aroian, R. V.; Sternberg, P. W.

    1991-01-01

    The let-23 gene, which encodes a putative tyrosine kinase of the epidermal growth factor (EGF) receptor subfamily, has multiple functions during Caenorhabditis elegans development. We show that let-23 function is required for vulval precursor cells (VPCs) to respond to the signal that induces vulval differentiation: a complete loss of let-23 function results in no induction. However, some let-23 mutations that genetically reduce but do not eliminate let-23 function result in VPCs apparently hypersensitive to inductive signal: as many as five of six VPCs can adopt vulval fates, in contrast to the three that normally do. These results suggest that the let-23 receptor tyrosine kinase controls two opposing pathways, one that stimulates vulval differentiation and another that negatively regulates vulval differentiation. Furthermore, analysis of 16 new let-23 mutations indicates that the let-23 kinase functions in at least five tissues. Since various let-23 mutant phenotypes can be obtained independently, the let-23 gene is likely to have tissue-specific functions. PMID:2071015

  18. interval functions

    Directory of Open Access Journals (Sweden)

    J. A. Chatfield

    1978-01-01

    Full Text Available Suppose N is a Banach space of norm |•| and R is the set of real numbers. All integrals used are of the subdivision-refinement type. The main theorem [Theorem 3] gives a representation of TH where H is a function from R×R to N such that H(p+,p+, H(p,p+, H(p−,p−, and H(p−,p each exist for each p and T is a bounded linear operator on the space of all such functions H. In particular we show that TH=(I∫abfHdα+∑i=1∞[H(xi−1,xi−1+−H(xi−1+,xi−1+]β(xi−1+∑i=1∞[H(xi−,xi−H(xi−,xi−]Θ(xi−1,xiwhere each of α, β, and Θ depend only on T, α is of bounded variation, β and Θ are 0 except at a countable number of points, fH is a function from R to N depending on H and {xi}i=1∞ denotes the points P in [a,b]. for which [H(p,p+−H(p+,p+]≠0 or [H(p−,p−H(p−,p−]≠0. We also define an interior interval function integral and give a relationship between it and the standard interval function integral.

  19. The mucolipin-2 (TRPML2) ion channel: a tissue-specific protein crucial to normal cell function.

    Science.gov (United States)

    Cuajungco, Math P; Silva, Joshua; Habibi, Ania; Valadez, Jessica A

    2016-02-01

    The discovery of the TRPML subfamily of ion channels has created an exciting niche in the fields of membrane trafficking, signal transduction, autophagy, and metal homeostasis. The TRPML protein subfamily consists of three members, TRPML1, TRPML2, and TRPML3, which are encoded by MCOLN1, MCOLN2, and MCOLN3 genes, respectively. They are non-selective cation channels with six predicted transmembrane domains and intracellular amino- and carboxyl-terminus regions. They localize to the plasma membrane, endosomes, and lysosomes of cells. TRPML1 is associated with the human lysosomal storage disease known as mucolipidosis type IV (MLIV), but TRPML2 and TRPML3 have not been linked with a human disease. Although TRPML1 is expressed in many tissues, TRPML3 is expressed in a varied but limited set of tissues, while TRPML2 has a more limited expression pattern where it is mostly detected in lymphoid and myeloid tissues. This review focuses on TRPML2 because it appears to play an important, yet unrecognized role in the immune system. While the evidence has been mostly indirect, we present and discuss relevant data that strengthen the connection of TRPML2 with cellular immunity. We also discuss the functional redundancy between the TRPML proteins, and how such features could be exploited as a potential therapeutic strategy for MLIV disease. We present evidence that TRPML2 expression may complement certain phenotypic alterations in MLIV cells and briefly examine the challenges of functional complementation. In conclusion, the function of TRPML2 still remains obscure, but emerging data show that it may serve a critical role in immune cell development and inflammatory responses.

  20. Bessel functions

    CERN Document Server

    Nambudiripad, K B M

    2014-01-01

    After presenting the theory in engineers' language without the unfriendly abstraction of pure mathematics, several illustrative examples are discussed in great detail to see how the various functions of the Bessel family enter into the solution of technically important problems. Axisymmetric vibrations of a circular membrane, oscillations of a uniform chain, heat transfer in circular fins, buckling of columns of varying cross-section, vibrations of a circular plate and current density in a conductor of circular cross-section are considered. The problems are formulated purely from physical considerations (using, for example, Newton's law of motion, Fourier's law of heat conduction electromagnetic field equations, etc.) Infinite series expansions, recurrence relations, manipulation of expressions involving Bessel functions, orthogonality and expansion in Fourier-Bessel series are also covered in some detail. Some important topics such as asymptotic expansions, generating function and Sturm-Lioville theory are r...

  1. Algebraic functions

    CERN Document Server

    Bliss, Gilbert Ames

    1933-01-01

    This book, immediately striking for its conciseness, is one of the most remarkable works ever produced on the subject of algebraic functions and their integrals. The distinguishing feature of the book is its third chapter, on rational functions, which gives an extremely brief and clear account of the theory of divisors.... A very readable account is given of the topology of Riemann surfaces and of the general properties of abelian integrals. Abel's theorem is presented, with some simple applications. The inversion problem is studied for the cases of genus zero and genus unity. The chapter on t

  2. POLYNOMIAL FUNCTIONS

    Institute of Scientific and Technical Information of China (English)

    王雷

    2008-01-01

    <正>Polynomial functions are among the sim- plest expressions in algebra.They are easy to evaluate:only addition and repeated multipli- cation are required.Because of this,they are often used to approximate other more compli-

  3. Functional dyspepsia

    NARCIS (Netherlands)

    Kleibeuker, JH; Thijs, JC

    2004-01-01

    Purpose of review Functional dyspepsia is a common disorder, most of the time of unknown etiology and with variable pathophysiology. Therapy has been and still is largely empirical. Data from recent studies provide new clues for targeted therapy based on knowledge of etiology and pathophysiologic me

  4. Functions and Malfunctions of Mammalian DNA-Cytosine Deaminases.

    Science.gov (United States)

    Siriwardena, Sachini U; Chen, Kang; Bhagwat, Ashok S

    2016-10-26

    The AID/APOBEC family enzymes convert cytosines in single-stranded DNA to uracils, causing base substitutions and strand breaks. They are induced by cytokines produced during the body's inflammatory response to infections, and they help combat infections through diverse mechanisms. AID is essential for the maturation of antibodies and causes mutations and deletions in antibody genes through somatic hypermutation (SHM) and class-switch recombination (CSR) processes. One member of the APOBEC family, APOBEC1, edits mRNA for a protein involved in lipid transport. Members of the APOBEC3 subfamily in humans (APOBEC3A, APOBEC3B, APOBEC3C, APOBEC3D, APOBEC3F, APOBEC3G, and APOBEC3H) inhibit infections of viruses such as HIV-1, HBV, and HCV, and retrotransposition of endogenous retroelements through mutagenic and nonmutagenic mechanisms. There is emerging consensus that these enzymes can cause mutations in the cellular genome at replication forks or within transcription bubbles depending on the physiological state of the cell and the phase of the cell cycle during which they are expressed. We describe here the state of knowledge about the structures of these enzymes, regulation of their expression, and both the advantageous and deleterious consequences of their expression, including carcinogenesis. We highlight similarities among them and present a holistic view of their regulation and function.

  5. Function and regulation of plant major intrinsic proteins

    DEFF Research Database (Denmark)

    Popovic, Milan

    Arsenic is a metalloid that is toxic to living organisms. The use of arsenic-contaminated ground water for drinking and for irrigation in agriculture presents serious health problems for millions of people in many parts of the world. Arsenate (As(V)) and arsenite (As(III)), the two most widespread...... inorganic forms of arsenic in the environment, can be taken up by plants and thus enter the food chain. Once inside the root cells, As(V) is reduced to As(III) which is then extruded to the soil solution or bound to phytochelatins (PCs) and transported to the vacuole in an effort to accomplish...... vacuoles. In this study using Arabidopsis, the role of TIP subfamily in arsenic transport was examined together with the role of N-terminus in regulation of AtNIP5;1, which has previously been shown to transport As(III) in a yeast expression system. The results showed that AtTIP4;1 functions...

  6. TRIM-9 functions in the UNC-6/UNC-40 pathway to regulate ventral guidance

    Institute of Scientific and Technical Information of China (English)

    Song Song; Qinglan Ge; Jinbo Wang; Haiyang Chen; Sanyuan Tang; Junfeng Bi; Xia Li; Qi Xie; Xun Huang

    2011-01-01

    TRIpartite Motif (TRIM) family proteins are ring finger domain-containing, multi-domain proteins implicated in many biological processes.Members of the TRIM-9/C-I subfamily of TRIM proteins, including TRIM-9, MIDI and MID2, have neuronal functions and are associated with neurological diseases. To explore whether the functions of C-I TRIM proteins are conserved in invertebrates, we analyzed Caenorhabditis elegans and Drosophila trim-9 mutants. C. elegans trim-9 mutants exhibit defects in the ventral guidance of hermaphrodite specific neuron (HSN) and the touch neuron AVM. Further genetic analyses indicate that TRIM-9 participates in the UNC-6-UNC-40 attraction pathway.Asymmetric distribution of UNC-40 during HSN development is normal in trim-9 mutants. However, the asymmetric localization of MIG-10,a downstream effector of UNC-40, is abolished in trim-9 mutants. These results suggest that TRIM-9 functions upstream of MIG-1 0 in the UNC40 pathway. Moreover, we showed that TRIM-9 exhibits E3 ubiquitin ligase activity in vitro and this activity is important for TRIM-9 function in vivo. Additionally, we found that Drosophila trim-9 is required for the midline attraction of a group of sensory neuron axons. Over-expression of the Netrin/UNC-6 receptor Frazzled suppresses the guidance defects in trim-9 mutants. Our study reveals an evolutionarily conserved function of TRIM-9 in the UNC-40/Frazzled-mediated UNC-6/Netrin attraction pathway.

  7. Functional and evolutionary analysis of DXL1, a non-essential gene encoding a 1-deoxy-D-xylulose 5-phosphate synthase like protein in Arabidopsis thaliana.

    Science.gov (United States)

    Carretero-Paulet, Lorenzo; Cairó, Albert; Talavera, David; Saura, Andreu; Imperial, Santiago; Rodríguez-Concepción, Manuel; Campos, Narciso; Boronat, Albert

    2013-07-15

    The synthesis of 1-deoxy-D-xylulose 5-phosphate (DXP), catalyzed by the enzyme DXP synthase (DXS), represents a key regulatory step of the 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway for isoprenoid biosynthesis. In plants DXS is encoded by small multigene families that can be classified into, at least, three specialized subfamilies. Arabidopsis thaliana contains three genes encoding proteins with similarity to DXS, including the well-known DXS1/CLA1 gene, which clusters within subfamily I. The remaining proteins, initially named DXS2 and DXS3, have not yet been characterized. Here we report the expression and functional analysis of A. thaliana DXS2. Unexpectedly, the expression of DXS2 failed to rescue Escherichia coli and A. thaliana mutants defective in DXS activity. Coherently, we found that DXS activity was negligible in vitro, being renamed as DXL1 following recent nomenclature recommendation. DXL1 is targeted to plastids as DXS1, but shows a distinct expression pattern. The phenotypic analysis of a DXL1 defective mutant revealed that the function of the encoded protein is not essential for growth and development. Evolutionary analyses indicated that DXL1 emerged from DXS1 through a recent duplication apparently specific of the Brassicaceae lineage. Divergent selective constraints would have affected a significant fraction of sites after diversification of the paralogues. Furthermore, amino acids subjected to divergent selection and likely critical for functional divergence through the acquisition of a novel, although not yet known, biochemical function, were identified. Our results provide with the first evidences of functional specialization at both the regulatory and biochemical level within the plant DXS family.

  8. P(1B)-ATPases--an ancient family of transition metal pumps with diverse functions in plants.

    Science.gov (United States)

    Williams, Lorraine E; Mills, Rebecca F

    2005-10-01

    P(1B)-ATPases form a distinct evolutionary sub-family of P-type ATPases, transporting transition metals such as Cu, Zn, Cd, Pb and Co across membranes in a wide range of organisms, including plants. Structurally they are distinct from other P-types, possessing eight transmembrane helices, a CPx/SPC motif in transmembrane domain six, and putative transition metal-binding domains at the N- and/or C-termini. Arabidopsis has eight P(1B)-ATPases (AtHMA1-AtHMA8), which differ in their structure, function and regulation. They perform a variety of important physiological tasks relating to transition metal transport and homeostasis. The crucial roles of plant P(1B)-ATPases in micronutrient nutrition, delivery of essential metals to target proteins, and toxic metal detoxification are discussed.

  9. Functional Organometallics

    Institute of Scientific and Technical Information of China (English)

    K.H.DTZ

    2007-01-01

    1 Results The lecture will address aspects of functional organometallics related to the development of novel organometallic materials.In chromium complexes of fused arenes-regio-and diastereoselectively accessible by chromium-templated benzannulation of arylcarbenes by alkynes[1]-a haptotropic migration of the chromium fragment along the π-face of fused arenes is controlled by both thermodynamics and the substitution pattern of the arene and the metal coligand sphere,and can be applied towards an organo...

  10. Functional Literacy

    Directory of Open Access Journals (Sweden)

    Fani Nolimal

    2000-12-01

    Full Text Available The author first defines literacy as the ability of co-operation in all fields of life and points at the features of illiterate or semi-literate individuals. The main stress is laid upon the assessment of literacy and illiteracy. In her opinion the main weak­ ness of this kind of evaluation are its vague psycho-metric characteristics, which leads to results valid in a single geographical or cultural environment only. She also determines the factors causing illiteracy, and she states that the level of functional literacy is more and more becoming a national indicator of successfulness.

  11. Lung function

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    2005200 The effect of body position changes on lung function, lung CT imaging and pathology in an oleic acid induced acute lung injury model. JI Xin-ping (戢新平), et al. Dept Emergency, 1st Affili Hosp, China Med Univ, Shenyang 110001. Chin J Tuberc Respir Dis, 2005;28(1) :33-36. Objective: To study the effect of body position changes on lung mechanics, oxygenation, CT images and pathology in an oleic acid-induced acute lung injury (ALl) model. Methods: The study groups con-

  12. Separation of stem cell maintenance and transposon silencing functions of Piwi protein.

    Science.gov (United States)

    Klenov, Mikhail S; Sokolova, Olesya A; Yakushev, Evgeny Y; Stolyarenko, Anastasia D; Mikhaleva, Elena A; Lavrov, Sergey A; Gvozdev, Vladimir A

    2011-11-15

    Piwi-interacting RNAs (piRNAs) and Piwi proteins have the evolutionarily conserved function of silencing of repetitive genetic elements in germ lines. The founder of the Piwi subfamily, Drosophila nuclear Piwi protein, was also shown to be required for the maintenance of germ-line stem cells (GSCs). Hence, null mutant piwi females exhibit two types of abnormalities, overexpression of transposons and severely underdeveloped ovaries. It remained unknown whether the failure of GSC maintenance is related to transposon derepression or if GSC self-renewal and piRNA silencing are two distinct functions of the Piwi protein. We have revealed a mutation, piwi(Nt), removing the nuclear localization signal of the Piwi protein. piwi(Nt) females retain the ability of GSC self-renewal and a near-normal number of egg chambers in the ovarioles but display a drastic transposable element derepression and nuclear accumulation of their transcripts in the germ line. piwi(Nt) mutants are sterile most likely because of the disturbance of piRNA-mediated transposon silencing. Analysis of chromatin modifications in the piwi(Nt) ovaries indicated that Piwi causes chromatin silencing only of certain types of transposons, whereas others are repressed in the nuclei without their chromatin modification. Thus, Piwi nuclear localization that is required for its silencing function is not essential for the maintenance of GSCs. We suggest that the Piwi function in GSC self-renewal is independent of transposon repression and is normally realized in the cytoplasm of GSC niche cells.

  13. Functional Cooperativity between ABCG4 and ABCG1 Isoforms.

    Directory of Open Access Journals (Sweden)

    Zoltán Hegyi

    Full Text Available ABCG4 belongs to the ABCG subfamily, the members of which are half transporters composed of a single transmembrane and a single nucleotide-binding domain. ABCG proteins have a reverse domain topology as compared to other mammalian ABC transporters, and have to form functional dimers, since the catalytic sites for ATP binding and hydrolysis, as well as the transmembrane domains are composed of distinct parts of the monomers. Here we demonstrate that ABCG4 can form homodimers, but also heterodimers with its closest relative, ABCG1. Both the full-length and the short isoforms of ABCG1 can dimerize with ABCG4, whereas the ABCG2 multidrug transporter is unable to form a heterodimer with ABCG4. We also show that contrary to that reported in some previous studies, ABCG4 is predominantly localized to the plasma membrane. While both ABCG1 and ABCG4 have been suggested to be involved in lipid transport or regulation, in accordance with our previous results regarding the long version of ABCG1, here we document that the expression of both the short isoform of ABCG1 as well as ABCG4 induce apoptosis in various cell types. This apoptotic effect, as a functional read-out, allowed us to demonstrate that the dimerization between these half transporters is not only a physical interaction but functional cooperativity. Given that ABCG4 is predominantly expressed in microglial-like cells and endothelial cells in the brain, our finding of ABCG4-induced apoptosis may implicate a new role for this protein in the clearance mechanisms within the central nervous system.

  14. The Role of the IL-20 Subfamily in Glaucoma

    Directory of Open Access Journals (Sweden)

    Mary K. Wirtz

    2016-01-01

    Full Text Available Glaucoma is a common disease that leads to loss of peripheral vision and, if left untreated, ultimately to blindness. While the exact cause(s of glaucoma is still unknown, two leading risk factors are age and elevated intraocular pressure. Several studies suggest a possible link between glaucoma and inflammation in humans and animal models. In particular, our lab recently identified a T104M mutation in IL-20 receptor-B (IL-20RB in primary open angle glaucoma patients from a large pedigree. Several of the interleukin- (IL- 20 family of cytokines and receptors are expressed in ocular tissues including the trabecular meshwork, optic nerve head, and retinal ganglion cells. The DBA/2J mouse develops high intraocular pressures with age and has characteristic optic nerve defects that make it a useful glaucoma model. IL-24 expression is significantly upregulated in the retina of these mice, while IL-20RA expression in the optic nerve is downregulated following pressure-induced damage. The identification of a mutation in the IL-20RB gene in a glaucoma pedigree and changes in expression levels of IL-20 family members in the DBA/2J mouse suggest that disruption of normal IL-20 signaling in the eye may contribute to degenerative processes associated with glaucoma.

  15. The Malesian species of the subfamily Maloideae (Rosaceae)

    NARCIS (Netherlands)

    Kalkman, C.

    1973-01-01

    Taxonomic revision, precursory to the treatment of the Rosaceae in Flora Malesiana. Generic limits in tribus Sorbeae are discussed, Stranvaesia is included in Photinia (5 spp. in Malesia), Micromeles (1 sp. in Malesia) is treated as generically different from Sorbus. Apart from these, there are in

  16. Molecular phylogeny of tribe Stachydeae (Lamiaceae subfamily Lamioideae)

    DEFF Research Database (Denmark)

    Salmaki, Yasaman; Zarre, Shahin; Ryding, Per Olof

    2013-01-01

    Although tribe Stachydeae (Lamiaceae) is considered monophyletic, relationships within the tribe are still poorly understood. The complexity of Stachydeae includes paraphyletic genera, considerable morphological plasticity, a range of ploidy levels, and presumably frequent natural hybridization. ...

  17. Children under 5 in Families and Subfamilies in 1990

    Data.gov (United States)

    U.S. Environmental Protection Agency — Variable was created as part of a set of indicators that demonstrate links between the condition of natural areas and human concerns and that quantify dependencies...

  18. Molecular phylogeny of tribe Stachydeae (Lamiaceae subfamily Lamioideae)

    DEFF Research Database (Denmark)

    Salmaki, Yasaman; Zarre, Shahin; Ryding, Per Olof

    2013-01-01

    Although tribe Stachydeae (Lamiaceae) is considered monophyletic, relationships within the tribe are still poorly understood. The complexity of Stachydeae includes paraphyletic genera, considerable morphological plasticity, a range of ploidy levels, and presumably frequent natural hybridization. ...

  19. Pterocarpus officinalis Jacq. Bloodwood Legumeminosae, Legume Family, lotoideae, Pea Subfamily

    Science.gov (United States)

    Peter L. Weaver

    1997-01-01

    Pterocarpus officinalis Jacq., called palo de pollo in Puerto Rico, bloodwood in Guyana and Panama, and by numerous other names throughout its extensive range, is an evergreen tree that reaches 40m in height

  20. Functional metamirrors

    CERN Document Server

    Asadchy, V S; Vehmas, J; Tretyakov, S A

    2014-01-01

    Conventional mirrors obey Snell's reflection law: a plane wave is reflected as a plane wave, at the same angle. To engineer spatial distributions of fields reflected from a mirror, one can either shape the reflector (for example, creating a parabolic reflector) or position some phase-correcting elements on top of a mirror surface (for example, designing a reflectarray antenna). Here we show, both theoretically and experimentally, that full-power reflection with general control over reflected wave phase is possible with a single-layer array of deeply sub-wavelength inclusions. These proposed artificial surfaces, metamirrors, provide various functions of shaped or nonuniform reflectors without utilizing any mirror. This can be achieved only if the forward and backward scattering of the inclusions in the array can be engineered independently, and we prove that it is possible using electrically and magnetically polarizable inclusions. The proposed sub-wavelength inclusions possess desired reflecting properties at...

  1. Functional analysis

    CERN Document Server

    Kesavan, S

    2009-01-01

    The material presented in this book is suited for a first course in Functional Analysis which can be followed by Masters students. While covering all the standard material expected of such a course, efforts have been made to illustrate the use of various theorems via examples taken from differential equations and the calculus of variations, either through brief sections or through exercises. In fact, this book will be particularly useful for students who would like to pursue a research career in the applications of mathematics. The book includes a chapter on weak and weak topologies and their applications to the notions of reflexivity, separability and uniform convexity. The chapter on the Lebesgue spaces also presents the theory of one of the simplest classes of Sobolev spaces. The book includes a chapter on compact operators and the spectral theory for compact self-adjoint operators on a Hilbert space. Each chapter has large collection of exercises at the end. These illustrate the results of the text, show ...

  2. Identification and in silico characterization of two novel genes encoding peptidases S8 found by functional screening in a metagenomic library of Yucatán underground water.

    Science.gov (United States)

    Apolinar-Hernández, Max M; Peña-Ramírez, Yuri J; Pérez-Rueda, Ernesto; Canto-Canché, Blondy B; De Los Santos-Briones, César; O'Connor-Sánchez, Aileen

    2016-11-15

    Metagenomics is a culture-independent technology that allows access to novel and potentially useful genetic resources from a wide range of unknown microorganisms. In this study, a fosmid metagenomic library of tropical underground water was constructed, and clones were functionally screened for extracellular proteolytic activity. One of the positive clones, containing a 41,614-bp insert, had two genes with 60% and 68% identity respectively with a peptidase S8 of Chitinimonas koreensis. When these genes were individually sub-cloned, in both cases their sub-clones showed proteolytic phenotype, confirming that they both encode functional proteases. These genes -named PrAY5 and PrAY6- are next to each other. They are similar in size (1845bp and 1824bp respectively) and share 66.5% identity. An extensive in silico characterization showed that their ORFs encode complex zymogens having a signal peptide at their 5' end, followed by a pro-peptide, a catalytic region, and a PPC domain at their 3' end. Their translated sequences were classified as peptidases S8A by sequence comparisons against the non-redundant database and corroborated by Pfam and MEROPS. Phylogenetic analysis of the catalytic region showed that they encode novel proteases that clustered with the sub-family S8_13, which according to the CDD database at NCBI, is an uncharacterized subfamily. They clustered in a clade different from the other three proteases S8 found so far by functional metagenomics, and also different from proteases S8 found in sequenced environmental samples, thereby expanding the range of potentially useful proteases that have been identified by metagenomics. I-TASSER modeling corroborated that they may be subtilases, thus possibly they participate in the hydrolysis of proteins with broad specificity for peptide bonds, and have a preference for a large uncharged residue in P1.

  3. Deciphering the molecular and functional basis of Dbl family proteins: a novel systematic approach toward classification of selective activation of the Rho family proteins.

    Science.gov (United States)

    Jaiswal, Mamta; Dvorsky, Radovan; Ahmadian, Mohammad Reza

    2013-02-08

    The diffuse B-cell lymphoma (Dbl) family of the guanine nucleotide exchange factors is a direct activator of the Rho family proteins. The Rho family proteins are involved in almost every cellular process that ranges from fundamental (e.g. the establishment of cell polarity) to highly specialized processes (e.g. the contraction of vascular smooth muscle cells). Abnormal activation of the Rho proteins is known to play a crucial role in cancer, infectious and cognitive disorders, and cardiovascular diseases. However, the existence of 74 Dbl proteins and 25 Rho-related proteins in humans, which are largely uncharacterized, has led to increasing complexity in identifying specific upstream pathways. Thus, we comprehensively investigated sequence-structure-function-property relationships of 21 representatives of the Dbl protein family regarding their specificities and activities toward 12 Rho family proteins. The meta-analysis approach provides an unprecedented opportunity to broadly profile functional properties of Dbl family proteins, including catalytic efficiency, substrate selectivity, and signaling specificity. Our analysis has provided novel insights into the following: (i) understanding of the relative differences of various Rho protein members in nucleotide exchange; (ii) comparing and defining individual and overall guanine nucleotide exchange factor activities of a large representative set of the Dbl proteins toward 12 Rho proteins; (iii) grouping the Dbl family into functionally distinct categories based on both their catalytic efficiencies and their sequence-structural relationships; (iv) identifying conserved amino acids as fingerprints of the Dbl and Rho protein interaction; and (v) defining amino acid sequences conserved within, but not between, Dbl subfamilies. Therefore, the characteristics of such specificity-determining residues identified the regions or clusters conserved within the Dbl subfamilies.

  4. Ether-à-go-go family voltage-gated K+ channels evolved in an ancestral metazoan and functionally diversified in a cnidarian–bilaterian ancestor

    Science.gov (United States)

    Li, Xiaofan; Martinson, Alexandra S.; Layden, Michael J.; Diatta, Fortunay H.; Sberna, Anna P.; Simmons, David K.; Martindale, Mark Q.; Jegla, Timothy J.

    2015-01-01

    We examined the evolutionary origins of the ether-à-go-go (EAG) family of voltage-gated K+ channels, which have a strong influence on the excitability of neurons. The bilaterian EAG family comprises three gene subfamilies (Eag, Erg and Elk) distinguished by sequence conservation and functional properties. Searches of genome sequence indicate that EAG channels are metazoan specific, appearing first in ctenophores. However, phylogenetic analysis including two EAG family channels from the ctenophore Mnemiopsis leidyi indicates that the diversification of the Eag, Erg and Elk gene subfamilies occurred in a cnidarian/bilaterian ancestor after divergence from ctenophores. Erg channel function is highly conserved between cnidarians and mammals. Here we show that Eag and Elk channels from the sea anemone Nematostella vectensis (NvEag and NvElk) also share high functional conservation with mammalian channels. NvEag, like bilaterian Eag channels, has rapid kinetics, whereas NvElk activates at extremely hyperpolarized voltages, which is characteristic of Elk channels. Potent inhibition of voltage activation by extracellular protons is conserved between mammalian and Nematostella EAG channels. However, characteristic inhibition of voltage activation by Mg2+ in Eag channels and Ca2+ in Erg channels is reduced in Nematostella because of mutation of a highly conserved aspartate residue in the voltage sensor. This mutation may preserve sub-threshold activation of Nematostella Eag and Erg channels in a high divalent cation environment. mRNA in situ hybridization of EAG channels in Nematostella suggests that they are differentially expressed in distinct cell types. Most notable is the expression of NvEag in cnidocytes, a cnidarian-specific stinging cell thought to be a neuronal subtype. PMID:25696816

  5. Ether-à-go-go family voltage-gated K+ channels evolved in an ancestral metazoan and functionally diversified in a cnidarian-bilaterian ancestor.

    Science.gov (United States)

    Li, Xiaofan; Martinson, Alexandra S; Layden, Michael J; Diatta, Fortunay H; Sberna, Anna P; Simmons, David K; Martindale, Mark Q; Jegla, Timothy J

    2015-02-15

    We examined the evolutionary origins of the ether-à-go-go (EAG) family of voltage-gated K(+) channels, which have a strong influence on the excitability of neurons. The bilaterian EAG family comprises three gene subfamilies (Eag, Erg and Elk) distinguished by sequence conservation and functional properties. Searches of genome sequence indicate that EAG channels are metazoan specific, appearing first in ctenophores. However, phylogenetic analysis including two EAG family channels from the ctenophore Mnemiopsis leidyi indicates that the diversification of the Eag, Erg and Elk gene subfamilies occurred in a cnidarian/bilaterian ancestor after divergence from ctenophores. Erg channel function is highly conserved between cnidarians and mammals. Here we show that Eag and Elk channels from the sea anemone Nematostella vectensis (NvEag and NvElk) also share high functional conservation with mammalian channels. NvEag, like bilaterian Eag channels, has rapid kinetics, whereas NvElk activates at extremely hyperpolarized voltages, which is characteristic of Elk channels. Potent inhibition of voltage activation by extracellular protons is conserved between mammalian and Nematostella EAG channels. However, characteristic inhibition of voltage activation by Mg(2+) in Eag channels and Ca(2+) in Erg channels is reduced in Nematostella because of mutation of a highly conserved aspartate residue in the voltage sensor. This mutation may preserve sub-threshold activation of Nematostella Eag and Erg channels in a high divalent cation environment. mRNA in situ hybridization of EAG channels in Nematostella suggests that they are differentially expressed in distinct cell types. Most notable is the expression of NvEag in cnidocytes, a cnidarian-specific stinging cell thought to be a neuronal subtype. © 2015. Published by The Company of Biologists Ltd.

  6. Functional mutagenesis screens reveal the 'cap structure' formation in disulfide-bridge free TASK channels.

    Science.gov (United States)

    Goldstein, Matthias; Rinné, Susanne; Kiper, Aytug K; Ramírez, David; Netter, Michael F; Bustos, Daniel; Ortiz-Bonnin, Beatriz; González, Wendy; Decher, Niels

    2016-01-22

    Two-pore-domain potassium (K2P) channels have a large extracellular cap structure formed by two M1-P1 linkers, containing a cysteine for dimerization. However, this cysteine is not present in the TASK-1/3/5 subfamily. The functional role of the cap is poorly understood and it remained unclear whether K2P channels assemble in the domain-swapped orientation or not. Functional alanine-mutagenesis screens of TASK-1 and TRAAK were used to build an in silico model of the TASK-1 cap. According to our data the cap structure of disulfide-bridge free TASK channels is similar to that of other K2P channels and is most likely assembled in the domain-swapped orientation. As the conserved cysteine is not essential for functional expression of all K2P channels tested, we propose that hydrophobic residues at the inner leaflets of the cap domains can interact with each other and that this way of stabilizing the cap is most likely conserved among K2P channels.

  7. TAWAWA1, a regulator of rice inflorescence architecture, functions through the suppression of meristem phase transition.

    Science.gov (United States)

    Yoshida, Akiko; Sasao, Masafumi; Yasuno, Naoko; Takagi, Kyoko; Daimon, Yasufumi; Chen, Ruihong; Yamazaki, Ryo; Tokunaga, Hiroki; Kitaguchi, Yoshinori; Sato, Yutaka; Nagamura, Yoshiaki; Ushijima, Tomokazu; Kumamaru, Toshihiro; Iida, Shigeru; Maekawa, Masahiko; Kyozuka, Junko

    2013-01-08

    Inflorescence structures result from the activities of meristems, which coordinate both the renewal of stem cells in the center and organ formation at the periphery. The fate of a meristem is specified at its initiation and changes as the plant develops. During rice inflorescence development, newly formed meristems acquire a branch meristem (BM) identity, and can generate further meristems or terminate as spikelets. Thus, the form of rice inflorescence is determined by a reiterative pattern of decisions made at the meristems. In the dominant gain-of-function mutant tawawa1-D, the activity of the inflorescence meristem (IM) is extended and spikelet specification is delayed, resulting in prolonged branch formation and increased numbers of spikelets. In contrast, reductions in TAWAWA1 (TAW1) activity cause precocious IM abortion and spikelet formation, resulting in the generation of small inflorescences. TAW1 encodes a nuclear protein of unknown function and shows high levels of expression in the shoot apical meristem, the IM, and the BMs. TAW1 expression disappears from incipient spikelet meristems (SMs). We also demonstrate that members of the SHORT VEGETATIVE PHASE subfamily of MADS-box genes function downstream of TAW1. We thus propose that TAW1 is a unique regulator of meristem activity in rice and regulates inflorescence development through the promotion of IM activity and suppression of the phase change to SM identity.

  8. Molecular characterization, functional expression, tissue localization and protective potential of a Taenia solium fatty acid-binding protein.

    Science.gov (United States)

    Illescas, Oscar; Carrero, Julio C; Bobes, Raúl J; Flisser, Ana; Rosas, Gabriela; Laclette, Juan P

    2012-12-01

    The fatty acid-binding proteins (FABPs) comprise a family of proteins that are widely expressed in animal cells and perform a variety of vital functions. Here, we report the identification, characterization, recombinant expression, tissue localization and protective potential of a Taenia solium FABP (TsFABP1). The TsFABP1 primary structure showed all the conserved residues characteristic of the subfamily iv of the intracellular Lipid-Binding Proteins (iLBPs), including those involved in the binding stabilization of the fatty acid molecule. Through a competitive binding assay we found that TsFABP1 is able to bind at least six different fatty acids with preference toward palmitic and stearic acid, suggesting that TsFABP1 is a member of the iLBP subfamily iv. Immunolocalization assays carried out on larval and adult tissues of four species of taeniids using anti-TsFABP1 hyperimmune sera produced in mice and rabbit, showed intense labeling in the tegument of the spiral canal and in subtegumental cytons of the larvae. These findings suggest that the spiral canal might be a major place for FA uptake in the developing scolex. In contrast, only subtegumental cytons in the adult worms stained positive. We propose that TsFABP1 is involved in the mechanism to mobilize fatty acids between compartments in the extensive syncytial tissue of taeniids. Protection assays carried out in a murine model of cysticercosis showed that subcutaneous immunization with TsFABP1 resulted in about 45% reduction of parasite load against an intraperitoneal challenge with Taenia crassiceps cysts. This reduction in parasite load correlated with the level of cellular and humoral immune responses against TsFABP1, as determined in spleen lymphocyte proliferation and ELISA testing.

  9. CRTC1 Function During Memory Encoding Is Disrupted in Neurodegeneration.

    Science.gov (United States)

    Parra-Damas, Arnaldo; Chen, Meng; Enriquez-Barreto, Lilian; Ortega, Laura; Acosta, Sara; Perna, Judith Camats; Fullana, M Neus; Aguilera, José; Rodríguez-Alvarez, José; Saura, Carlos A

    2017-01-15

    Associative memory impairment is an early clinical feature of dementia patients, but the molecular and cellular mechanisms underlying these deficits are largely unknown. In this study, we investigated the functional regulation of the cyclic adenosine monophosphate response element binding protein (CREB)-regulated transcription coactivator 1 (CRTC1) by associative learning in physiological and neurodegenerative conditions. We evaluated the activation of CRTC1 in the hippocampus of control mice and mice lacking the Alzheimer's disease-linked presenilin genes (presenilin conditional double knockout [PS cDKO]) after one-trial contextual fear conditioning by using biochemical, immunohistochemical, and gene expression analyses. PS cDKO mice display classical features of neurodegeneration occurring in Alzheimer's disease including age-dependent cortical atrophy, neuron loss, dendritic degeneration, and memory deficits. Context-associative learning, but not single context or unconditioned stimuli, induces rapid dephosphorylation (Ser151) and translocation of CRTC1 from the cytosol/dendrites to the nucleus of hippocampal neurons in the mouse brain. Accordingly, context-associative learning induces differential CRTC1-dependent transcription of c-fos and the nuclear receptor subfamily 4 (Nr4a) genes Nr4a1-3 in the hippocampus through a mechanism that involves CRTC1 recruitment to CRE promoters. Deregulation of CRTC1 dephosphorylation, nuclear translocation, and transcriptional function are associated with long-term contextual memory deficits in PS cDKO mice. Importantly, CRTC1 gene therapy in the hippocampus ameliorates context memory and transcriptional deficits and dendritic degeneration despite ongoing cortical degeneration in this neurodegeneration mouse model. These findings reveal a critical role of CRTC1 in the hippocampus during associative memory, and provide evidence that CRTC1 deregulation underlies memory deficits during neurodegeneration. Copyright © 2016

  10. Structural and functional diversification in the teleost S100 family of calcium-binding proteins

    Directory of Open Access Journals (Sweden)

    Korsching Sigrun I

    2008-02-01

    Full Text Available Abstract Background Among the EF-Hand calcium-binding proteins the subgroup of S100 proteins constitute a large family with numerous and diverse functions in calcium-mediated signaling. The evolutionary origin of this family is still uncertain and most studies have examined mammalian family members. Results We have performed an extensive search in several teleost genomes to establish the s100 gene family in fish. We report that the teleost S100 repertoire comprises fourteen different subfamilies which show remarkable similarity across six divergent teleost species. Individual species feature distinctive subsets of thirteen to fourteen genes that result from local gene duplications and gene losses. Eight of the fourteen S100 subfamilies are unique for teleosts, while six are shared with mammalian species and three of those even with cartilaginous fish. Several S100 family members are found in jawless fish already, but none of them are clear orthologs of cartilaginous or bony fish s100 genes. All teleost s100 genes show the expected structural features and are subject to strong negative selection. Many aspects of the genomic arrangement and location of mammalian s100 genes are retained in the teleost s100 gene family, including a completely conserved intron/exon border between the two EF hands. Zebrafish s100 genes exhibit highly specific and characteristic expression patterns, showing both redundancy and divergence in their cellular expression. In larval tissue expression is often restricted to specific cell types like keratinocytes, hair cells, ionocytes and olfactory receptor neurons as demonstrated by in situ hybridization. Conclusion The origin of the S100 family predates at least the segregation of jawed from jawless fish and some extant family members predate the divergence of bony from cartilaginous fish. Despite a complex pattern of gene gains and losses the total repertoire size is remarkably constant between species. On the expression

  11. The swarming activity and the relationships between the termites in the Subfamily of Macrotermitinae and the fungi (Termitomyces) in Yunnan%云南大白蚁亚科白蚁分飞情况及与蚁巢伞关系

    Institute of Scientific and Technical Information of China (English)

    何银竹; 刘蓓; 梁醒财

    2009-01-01

    在云南绿春观察大白蚁亚科4种土白蚁的分飞活动,研究大白蚁亚科白蚁和蚁巢伞之间的关系,得知:大白蚁亚科不同种类白蚁分飞孔形状不相同,分飞时分布于孔口周围的白蚁型、数目和扩散范围存在差异,这些蚁巢的外露特征可以作为白蚁种类识别的辅助依据.采集32巢白蚁以及其巢上生长的蚁巢伞,结果显示,大白蚁亚科每一个白蚁巢仅生长一种蚁巢伞 Termitomyces子实体.与小果蚁巢伞共生的白蚁也与其他蚁巢伞共生,推测真菌能改变白蚁的行为.对白蚁种类和蚁巢伞种类对应关系的研究表明在小地域内,白蚁和蚁巢伞不仅存在属间高度专一性,而且种间也显示较高的共生专一性.%The biology of four species of the subfamily Macrotermitinae in Luchun of Yunnan was studied. The results showed that some differences exist in the shape of exit holes, types, numbers and spreading distance of termites around the exit holes, which can be used for species identification. Our results also demonstrated that only one fungal species ( Termitomyces ) could be cultivated within a single termite colony. Termites that cultivate T. microcarpus also had symbiotic relationships with other fungi of the same genus. It is therefore speculated that termite behaviors could be changed when different fungi are cultivated. In addition, the investigation of interaction between termites and fungi indicated that, in a small area, high interactive specificity existed not only at the genus level, but also at the species level.

  12. Functional Programming in R

    DEFF Research Database (Denmark)

    Mailund, Thomas

    2017-01-01

    Master functions and discover how to write functional programs in R. In this book, you'll make your functions pure by avoiding side-effects; you’ll write functions that manipulate other functions, and you’ll construct complex functions using simpler functions as building blocks. In Functional...... functions by combining simpler functions. You will: Write functions in R including infix operators and replacement functions Create higher order functions Pass functions to other functions and start using functions as data you can manipulate Use Filer, Map and Reduce functions to express the intent behind...... code clearly and safely Build new functions from existing functions without necessarily writing any new functions, using point-free programming Create functions that carry data along with them...

  13. Characterization of the RND family of multidrug efflux pumps: in silico to in vivo confirmation of four functionally distinct subgroups.

    Science.gov (United States)

    Godoy, Patricia; Molina-Henares, Antonio J; de la Torre, Jesús; Duque, Estrella; Ramos, Juan L

    2010-11-01

    We have developed a generalized profile that identifies members of the root-nodulation-cell-division (RND) family of efflux pumps and classifies them into four functional subfamilies. According to Z-score values, efflux pumps can be grouped by their metabolic function, thus making it possible to distinguish pumps involved in antibiotic resistance (group 1) from those involved in metal resistance (group 3). In silico data regarding efflux pumps in group 1 were validated after identification of RND efflux pumps in a number of environmental microbes that were isolated as resistant to ethidium bromide. Analysis of the Pseudomonas putida KT2440 genome identified efflux pumps in all groups. A collection of mutants in efflux pumps and a screening platform consisting of 50 drugs were created to assign a function to the efflux pumps. We validated in silico data regarding efflux pumps in groups 1 and 3 using 9 different mutants. Four mutants belonging to group 2 were found to be more sensitive than the wild-type to oxidative stress-inducing agents such as bipyridyl and methyl viologen. The two remaining mutants belonging to group 4 were found to be more sensitive than the parental to tetracycline and one of them was particularly sensitive to rubidium and chromate. By effectively combining in vivo data with generalized profiles and gene annotation data, this approach allowed the assignment, according to metabolic function, of both known and uncharacterized RND efflux pumps into subgroups, thereby providing important new insight into the functions of proteins within this family.

  14. Special functions & their applications

    CERN Document Server

    Lebedev, N N

    1972-01-01

    Famous Russian work discusses the application of cylinder functions and spherical harmonics; gamma function; probability integral and related functions; Airy functions; hyper-geometric functions; more. Translated by Richard Silverman.

  15. Functions of bounded variation

    OpenAIRE

    Lind, Martin

    2006-01-01

    The paper begins with a short survey of monotone functions. The functions of bounded variation are introduced and some basic properties of these functions are given. Finally the jump function of a function of bounded variation is defined.

  16. Relations between Lipschitz functions and convex functions

    Institute of Scientific and Technical Information of China (English)

    RUAN Yingbin

    2005-01-01

    We discuss the relationship between Lipschitz functions and convex functions.By these relations, we give a sufficient condition for the set of points where Lipschitz functions on a Hilbert space is Frechet differentiable to be residual.

  17. Gaussian Functions, Γ-Functions and Wavelets

    Institute of Scientific and Technical Information of China (English)

    蔡涛; 许天周

    2003-01-01

    The relations between Gaussian function and Γ-function is revealed first at one-dimensional situation. Then, the Fourier transformation of n-dimensional Gaussian function is deduced by a lemma. Following the train of thought in one-dimensional situation, the relation between n-dimensional Gaussian function and Γ-function is given. By these, the possibility of arbitrary derivative of an n-dimensional Gaussian function being a mother wavelet is indicated. The result will take some enlightening role in exploring the internal relations between Gaussian function and Γ-function as well as in finding high-dimensional mother wavelets.

  18. The Lipid Transfer Protein StarD7: Structure, Function, and Regulation

    OpenAIRE

    Susana Genti-Raimondi; Panzetta-Dutari, Graciela M.; Sofía Angeletti; Viviana Rena; Jésica Flores-Martin

    2013-01-01

    The steroidogenic acute regulatory (StAR) protein-related lipid transfer (START) domain proteins constitute a family of evolutionarily conserved and widely expressed proteins that have been implicated in lipid transport, metabolism, and signaling. The 15 well-characterized mammalian START domain-containing proteins are grouped into six subfamilies. The START domain containing 7 mRNA encodes StarD7, a member of the StarD2/phosphatidylcholine transfer protein (PCTP) subfamily, which was first i...

  19. The Lipid Transfer Protein StarD7: Structure, Function, and Regulation

    OpenAIRE

    Susana Genti-Raimondi; Panzetta-Dutari, Graciela M.; Sofía Angeletti; Viviana Rena; Jésica Flores-Martin

    2013-01-01

    The steroidogenic acute regulatory (StAR) protein-related lipid transfer (START) domain proteins constitute a family of evolutionarily conserved and widely expressed proteins that have been implicated in lipid transport, metabolism, and signaling. The 15 well-characterized mammalian START domain-containing proteins are grouped into six subfamilies. The START domain containing 7 mRNA encodes StarD7, a member of the StarD2/phosphatidylcholine transfer protein (PCTP) subfamily, which was first i...

  20. Functional Pairing of Class B1 Ligand-GPCR in Cephalochordate Provides Evidence of the Origin of PTH and PACAP/Glucagon Receptor Family.

    Science.gov (United States)

    On, Jason S W; Duan, Cumming; Chow, Billy K C; Lee, Leo T O

    2015-08-01

    Several hypotheses have been proposed regarding the origin and evolution of the secretin family of peptides and receptors. However, identification of homologous ligand-receptor pairs in invertebrates and vertebrates is difficult because of the low levels of sequence identity between orthologs of distant species. In this study, five receptors structurally related to the vertebrate class B1 G protein-coupled receptor (GPCR) family were characterized from amphioxus (Branchiostoma floridae). Phylogenetic analysis showed that they clustered with vertebrate parathyroid hormone receptors (PTHR) and pituitary adenylate cyclase-activating polypeptide (PACAP)/glucagon receptors. These PTHR-like receptors shared synteny with several PTH and PACAP/glucagon receptors identified in spotted gar, Xenopus, and human, indicating that amphioxus preserves the ancestral chordate genomic organization of these receptor subfamilies. According to recent data by Mirabeau and Joly, amphioxus also expresses putative peptide ligands including homologs of PTH (bfPTH1 and 2) and PACAP/GLUC-like peptides (bfPACAP/GLUCs) that may interact with these receptors. Functional analyses showed that bfPTH1 and bfPTH2 activated one of the amphioxus receptors (bf98C) whereas bfPACAP/GLUCs strongly interacted with bf95. In summary, our data confirm the presence of PTH and PACAP/GLUC ligand-receptor pairs in amphioxus, demonstrating that functional homologs of vertebrate PTH and PACAP/glucagon GPCR subfamilies arose before the cephalochordate divergence from the ancestor of tunicates and vertebrates. © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  1. On quasinearly subharmonic functions

    OpenAIRE

    Dovgoshey, O.; Riihentaus, J.

    2016-01-01

    We recall the definition of quasinearly subharmonic functions, point out that this function class includes, among others, subharmonic functions, quasisubharmonic functions, nearly subharmonic functions and essentially almost subharmonic functions. It is shown that the sum of two quasinearly subharmonic functions may not be quasinearly subharmonic. Moreover, we characterize the harmonicity via quasinearly subharmonicity.

  2. Physiologic and pathophysiologic consequences of altered sialylation and glycosylation on ion channel function.

    Science.gov (United States)

    Baycin-Hizal, Deniz; Gottschalk, Allan; Jacobson, Elena; Mai, Sunny; Wolozny, Daniel; Zhang, Hui; Krag, Sharon S; Betenbaugh, Michael J

    2014-10-17

    Voltage-gated ion channels are transmembrane proteins that regulate electrical excitability in cells and are essential components of the electrically active tissues of nerves, muscle and the heart. Potassium channels are one of the largest subfamilies of voltage sensitive channels and are among the most-studied of the voltage-gated ion channels. Voltage-gated channels can be glycosylated and changes in the glycosylation pattern can affect ion channel function, leading to neurological and neuromuscular disorders and congenital disorders of glycosylation (CDG). Alterations in glycosylation can also be acquired and appear to play a role in development and aging. Recent studies have focused on the impact of glycosylation and sialylation on ion channels, particularly for voltage-gated potassium and sodium channels. The terminal step of sialylation often affects channel activation and inactivation kinetics. The presence of sialic acids on O or N-glycans can alter the gating mechanism and cause conformational changes in the voltage-sensing domains due to sialic acid's negative charges. This manuscript will provide an overview of sialic acids, potassium and sodium channel function, and the impact of sialylation on channel activation and deactivation.

  3. Molecular characterization and functional analysis of IRF3 in tilapia (Oreochromis niloticus).

    Science.gov (United States)

    Gu, Yi-Feng; Wei, Qun; Tang, Shou-Jie; Chen, Xiao-Wu; Zhao, Jin-Liang

    2016-02-01

    Interferon regulatory factor 3 (IRF3) plays a key role in interferon (IFN) response and binding to the IFN stimulatory response elements (ISREs) within the promoter of IFN and IFN-stimulated genes followed by virus infection. In the current study, we discovered one IRF3 homologue in tilapia genome and analyzed the characterizations and functions of tilapia IRF3. Tilapia IRF3 contains 1368 bp with an ORF of 455 aa. Structurally, tilapia IRF3 protein typically shares the conserved characterizations with other species' IRF3 homologues, displaying conserved DNA-binding domain, IRF association domain, serine-rich C terminal domain, and tryptophan residue cluster. Phylogenetic analysis illustrated that tilapia IRF3 belongs to the IRF3 subfamily. Real-time PCR revealed a broad expression pattern of tilapia IRF3 in various tissues. Subcellular localization analysis showed that tilapia IRF3 mainly resides in the cytoplasm, Western blot demonstrated that IRF3 was distributed in the cytoplasmic fraction. Functionally, IRF3 was found to be transcriptionally up-regulated by the poly I:C stimulation. Moreover, reporter assay elucidated that tilapia IRF3 serves as a regulator in mediating IFN response by increasing the activity of IFN-β and ISRE-containing promoter. These data supported the view that tilapia IRF3 is a potential molecule in IFN immune defense system against viral infection.

  4. Proteoliposomes as Tool for Assaying Membrane Transporter Functions and Interactions with Xenobiotics

    Directory of Open Access Journals (Sweden)

    Annamaria Tonazzi

    2013-09-01

    Full Text Available Proteoliposomes represent a suitable and up to date tool for studying membrane transporters which physiologically mediate absorption, excretion, trafficking and reabsorption of nutrients and metabolites. Using recently developed reconstitution strategies, transporters can be inserted in artificial bilayers with the same orientation as in the cell membranes and in the absence of other interfering molecular systems. These methodologies are very suitable for studying kinetic parameters and molecular mechanisms. After the first applications on mitochondrial transporters, in the last decade, proteoliposomes obtained with optimized methodologies have been used for studying plasma membrane transporters and defining their functional and kinetic properties and structure/function relationships. A lot of information has been obtained which has clarified and completed the knowledge on several transporters among which the OCTN sub-family members, transporters for neutral amino acid, B0AT1 and ASCT2, and others. Transporters can mediate absorption of substrate-like derivatives or drugs, improving their bioavailability or can interact with these compounds or other xenobiotics, leading to side/toxic effects. Therefore, proteoliposomes have recently been used for studying the interaction of some plasma membrane and mitochondrial transporters with toxic compounds, such as mercurials, H2O2 and some drugs. Several mechanisms have been defined and in some cases the amino acid residues responsible for the interaction have been identified. The data obtained indicate proteoliposomes as a novel and potentially important tool in drug discovery.

  5. Phylogeny, Functional Annotation, and Protein Interaction Network Analyses of the Xenopus tropicalis Basic Helix-Loop-Helix Transcription Factors

    Directory of Open Access Journals (Sweden)

    Wuyi Liu

    2013-01-01

    Full Text Available The previous survey identified 70 basic helix-loop-helix (bHLH proteins, but it was proved to be incomplete, and the functional information and regulatory networks of frog bHLH transcription factors were not fully known. Therefore, we conducted an updated genome-wide survey in the Xenopus tropicalis genome project databases and identified 105 bHLH sequences. Among the retrieved 105 sequences, phylogenetic analyses revealed that 103 bHLH proteins belonged to 43 families or subfamilies with 46, 26, 11, 3, 15, and 4 members in the corresponding supergroups. Next, gene ontology (GO enrichment analyses showed 65 significant GO annotations of biological processes and molecular functions and KEGG pathways counted in frequency. To explore the functional pathways, regulatory gene networks, and/or related gene groups coding for Xenopus tropicalis bHLH proteins, the identified bHLH genes were put into the databases KOBAS and STRING to get the signaling information of pathways and protein interaction networks according to available public databases and known protein interactions. From the genome annotation and pathway analysis using KOBAS, we identified 16 pathways in the Xenopus tropicalis genome. From the STRING interaction analysis, 68 hub proteins were identified, and many hub proteins created a tight network or a functional module within the protein families.

  6. Arrest functions of the MIF ligand/receptor axes in atherogenesis

    Directory of Open Access Journals (Sweden)

    Sabine eTillmann

    2013-05-01

    Full Text Available Macrophage migration inhibitory factor (MIF has been defined as an important chemokine-like function (CLF chemokine with an essential role in monocyte recruitment and arrest. Adhesion of monocytes to the vessel wall and their transendothelial migration are critical in atherogenesis and many other inflammatory diseases. Chemokines carefully control all steps of the monocyte recruitment process. Those chemokines specialized in controlling arrest are typically immobilized on the endothelial surface, mediating the arrest of rolling monocytes by chemokine receptor-triggered pathways. The chemokine receptor CXCR2 functions as an important arrest receptor on monocytes. An arrest function has been revealed for the bona fide CXCR2 ligands CXCL1 and CXCL8, but genetic studies also suggested that additional arrest chemokines are likely to be involved in ath